Chemistry, Biomolecules, and Enzymes

Table 3

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• Basic Chemistry– Elements and the Pe

riodic Table– Structure of an Atom– Isotopes

• Chemical Bonds– Covalent Bonds – Ionic Bonds– Hydrogen Bonds– Chemical Reactions

• Properties of Water

• Macromolecules– Lipids– Proteins– Carbohydrates– Nucleic Acids

• Enzymes – General– Substrate Specificity– Allosteric Regulation– Inhibitors

• Credits

Denotes a Review Song!

Elements and the Periodic Table

• Element- one of 92 substances that cannot be broken down by chemical reactions

• Atomic number- number of protons, equal to the number of electrons

• Mass number- number of protons +the number of neutrons

ElementName

AtomicNumber

ChemicalSymbol

Atomic Mass, Mass Number would be 23

Menu Structure of an Atom

Structure of an Atom

• Atom- smallest unit of matter that still retains the properties of a specific element

• Proton- positively charged, 1 AMU (atomic mass unit)

• Neutron- neutral charge, 1 AMU

• Electron- negatively charged, 1/2000 AMU

Menu IsotopesElements/Table

Isotopes

• Isotope- atom with the same number of protons, but different number of neutrons

• Radioactive Isotope- nucleus decays spontaneously, releasing particles and energy, may lead to a change in the number of protons, useful in radioactive dating (Carbon 14), following atoms through metabolism (PET scanners), diagnoses, but can damage cellular molecules

Menu Covalent BondsAtomic Structure

Covalent Bonds

• Covalent Bond- Sharing of one or more pairs of valence electrons between two atoms (Single Bond- one pair, Double Bond- two pairs)

• Molecule- 2 or more atoms held together by covalent bonds

• Electronegativity- how much an atom attracts electrons

Click to start video:

MenuIsotopes Covalent (cont.)

Covalent Bonds

• Non-Polar- between two atoms with the same electronegativity, electrons are shared equally

• Polar- between two atoms with different electronegativity, electron pair shared unequally between the two atoms, giving one a δ+ (slight positive charge), and one a δ- (slight negative charge)

MenuCovalent Bonds Ionic Bonds

Ionic Bonds/ Overview

• Ionic Bond- the transfer of a valence electron to a more electronegative atom

• Ion- a charged atom or molecule (cation is positive, and anion is negative)

• Ionic Compounds/Salts- formed by ionic bonds, don’t consist of molecules, form a crystal with a definite ratio of atoms

Overview of BondingClick to start video:

MenuCovalent Bonds Hydrogen Bonds

Hydrogen Bonds

• Hydrogen Bond- attraction between a slightly positive hydrogen of one molecule and a slightly negative oxygen (or other electronegative atom) of another molecule, individually weak, but strong when grouped together

Quick Review of Bonding: Time for a Song!

MenuIonic Bonds Chemical Reactions

Chemical Reactions

• Chemical Reaction- the making and breaking of chemical bonds, leading to a change in the composition of matter, most are reversible

• Reactants- starting materials• Products- ending materials• Will tend to reach

equilibrium, products and reactants are in a fixed ratio

Equilibrium Diagram

MenuHydrogen Bonds Properties of H2O

Properties of Water

• Good solvent (can dissolve other things) because it is polar and can form hydrogen bonds

• Is cohesive (can stick to other water) and adhesive (can stick to other molecules) because of hydrogen bonds

• Good medium for reaction, often an important reactant or product• High specific heat (takes a lot of energy to change its heat) and High

heat of vaporization (takes a lot of energy to go from a liquid to a gas, easy cooling by evaporation)

• Density is highest at 4 ｰ C because hydrogen bonds make the solid form of water create a crystalline lattice structure that takes up space, means that ice floats and because ice is a good insulator, water underneath it will stay warm

• High surface tension because of hydrogen bonds• Low friction/ is a good lubricant

MenuChemical Reactions Lipids

Lipids

• Examples: phospholipids, cholesterol, estrogen, wax

• Made up of glycerol and fatty acids or a steroid core (4 rings)

• Store energy, build membranes, insulate, serve as hormones, some are vitamins (example: vitamin E)

• Cholesterol used to build all other steroid molecules

Glycerol

Fatty Acid Tails

MenuProperties of H2O Proteins

Proteins• Made up of amino acids, which all have an amino group, carboxyl group,

and one of 20 possible different R groups• Joined together by peptide bonds between carboxyl and amino groups• Levels of Structure

– Primary (1 ｰ ) - sequence and types of amino acids used in a protein– Secondary (2 ｰ )- shape (α –helix, β- pleated sheet) that different sections of

the protein strand will take based on hydrogen bonds (between R- groups)– Tertiary (3 ｰ )- 3D shape of protein caused by hydrogen bonds and other

bonds between R-groups– Quaternary (4 ｰ )- how 2+ protein strands (polypeptides) wrap together to

form 1 large complex

• Make up many functional and structural parts of cells, also are enzymes to do chemical reactions

MenuLipids Protein Diagrams

Proteins (Diagrams)

MenuProteins Carbohydrates

Carbohydrates

• Examples: glucose, starch, cellulose, sucrose

• Made up of monosaccharides (single sugars such as glucose and fructose), form dissacharides (double sugars such as sucrose and lactose) or polysaccharides (many sugars such as cellulose, starch (plant= amylose, animal= glycogen, chitin))

• Store short and long term energy, form structures such as cell walls

Amylose, a form of starch found in plants, a polysaccharide

MenuProtein Diagrams Nucleic Acids

Nucleic Acids

• Made up of nucleotides, which are made of a phosphate group, a 5 carbon sugar, and one of 4 possible nitrogenous bases (for DNA= adenine, guanine, cytosine, thymine, for RNA= adenine, guanine, cytosine, uracil)

• Hold/ transfer instructions of how to build proteins (genetic information)

• ATP transfers/stores energy (for a few seconds

MenuCarbohydrates Nucleic Acids (cont.)

Quick Review of Biomolecules: Time for a Song!

Nucleic Acids

• Form chains when the phosphate of one nucleotide joins to the sugar of another nucleotide

• Another chain is held to the first by hydrogen bonds between the bases, and the two strands twist into a double helix

• Strands are antiparallel

MenuNucleic Acids Enzymes (General)

Enzymes (General)

• Speed up metabolic reactions by lowering energy barriers

• Enzyme = macromolecule that acts as a catalyst

• Catalyst = chemical agent that speeds up a reaction without being consumed

• Activation Energy = initial energy required for starting a reaction, often supplied as heat

• Transition state = unstable form of reactants once they have absorbed enough energy for bonds to break

• An enzyme catalyzes a reaction by lowering the Activation Energy Barrier, enabling the reactant molecules to reach their transition state more often

MenuNucleic Acids Diagram of Reaction

Diagram of a Reaction

MenuEnzymes (General) Substrate Specificity

Substrate Specificity

• Substrate = reactant an enzyme acts on, converts substrate to product

• Enzyme-Substrate Complex = forms when enzyme and substrate join

• Enzyme will only act on its specific substrate – dependent on shape

• Active Site = region of enzyme that substrate binds to

• Induced fit = enzyme changes shape to fit more snugly into substrate

Click to start video:

MenuDiagram of Reaction Allosteric Regulation

Allosteric Regulation

• A protein’s function at one site is affected by the binding of a regulatory molecule to a separate site

• Allosteric Activator = binds to regulatory site and stabilizes the shape that has functional active sites

• Allosteric Inhibitor = binds to regulatory site and stabilizes inactive form of enzyme

• Cooperativity = mechanism that amplifies the response of enzymes to substrates by triggering shape change (and thus catalysis) in all subunits of an enzyme

• Feedback Inhibition = metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway

MenuSubstrate Specificity Regulation (cont.)

Allosteric Regulationallosteric inhibitor

MenuAllosteric Regulation Inhibitors

Inhibitors

• Competitive Inhibitors= mimic normal substrate molecules and block substrate from active site by binding to active site

• Noncompetitive Inhibitors= impede enzymatic reactions by binding to another part of the enzyme, altering its shape

Quick Review of Enzymes: Time for a Song!

MenuAllosteric Regulation Credits

Biomolecule Review SongChorus:Carbohydrates, Nucleic Acids,Proteins, Lipids,Are your passesTo keep you working properlyThese are the molecules that you need

There’s 4 types4 types4 types of biomolecules you need

Verse 1:Lipids they’re your body’s fatsYou saw them when we dissected catsThe phosphate heads of the bilayerThey sure like to touch waterThey’re on the outside of the cellThe fatty acid tails are protected well

Verse 2:Proteins are the building blocksOf your body’s many partsThey’ve got carboxyl and amino groupsAnd 20 possible R groups tooIf amino acids make a chainPrimary structure is its nameSecondary they fold upTertiary is a 3D clumpQuaternary they join togetherTo build the final protein structure

Verse 3:Mono and disaccharridesAre carbohydrates in disguiseThey store short term energyFrom foods that are very sugary

Nucleic Acids have a phosphate5 carbon sugar and nitrogen baseThey make up your DNAATP and RNAThey’ve got two strands antiparallelAnd carry genetic info as well

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Enzyme Review SongChorus:EnzymesThey can catalyzeChemical reactionsWhen they bind at their active siteAnd substratesHave a specific shapeFor the enzyme That fits into them the right way

Verse 1:Activation energy a reaction needsTo start forcefullyIt forms a barrier of energy requiredTo break the bonds that hold reactants together

But then the enzymeIt comes just in timeAnd saves the dayIt lowers the barrierTo reach the transition stateReactants unstableReaction underway

Verse 2:Enzyme inhibitorsThey attempt to blockThe enzyme-substrate lockSome compete directlyAnd some do notWith the enzyme that they want to stop

Enzymes they regulateInhibit or activateAllostericallyThey can change the shapeOf a protein so that it mayStabilize its active sitesOr just inactivate

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Bonding Review SongVerse:Just an ionic bondTransfer of electronsIt lets atoms fillThose last valence spots

ElectronegativityTo the higher one electrons fleeIonic bonds oh they can giveMetallic properties

And then there’s covalent bondsThey can share electronsThey make non-metals strongTo last on and on and on and on

Some bonds are polarElectrons shared unequallyDue to differentElectronegativities

Hydrogen bondsThey are weak one-on-oneBut togetherThey are strong!

Chorus:Don’t stop bondingHold on to those electronsTo keep that moleculeHolding strong

Ionic, CovalentAnd Hydrogen bonding they makeMolecules stayIn their place

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Credits• Atom Cover Art: http://www.presentermedia.com/files/clipart/00001000/1474• Structure of a Carbon Atom: http://www.universetoday.com/wp-content/uploads/2010/02/c-atom_e1.gif• Helium Isotopes: http://www.green-planet-solar-energy.com/images/helium-isotopes-5-to-8.gif• Covalent Bond Video: http://www.youtube.com/watch?v=1wpDicW_MQQ• Picture of Water Molecule: http://media.wiley.com/Lux/33/168033.image0.jpg• Electronegativity Video: http://www.youtube.com/watch?v=Kj3o0XvhVqQ• Hydrogen Bond Diagram: http://academic.brooklyn.cuny.edu/biology/bio4fv/page/image12.gif• Equilibrium Diagram: http://www.bbc.co.uk/scotland/learning/bitesize/higher/chemistry/images/process_of_equilibrium.jpg• Protein Structure Diagram: http://www.umass.edu/molvis/workshop/imgs/protein-structure2.png• Nucleotide Diagram: http://www.buzzle.com/img/articleImages/387160-1237-22.jpg• Amylose Diagram: http://www.mansfield.ohio-state.edu/~sabedon/071amylo.gif• Antiparallel DNA Diagram: http://www.tokresource.org/tok_classes/biobiobio/biomenu/dna_structure/dsDNA.jpgD• Diagram of a Reaction: http://www4.nau.edu/meteorite/Meteorite/Images/activation-energy.png• Enzyme-Substrate Video: http://www.youtube.com/watch?v=V4OPO6JQLO• Allosteric Regulation Diagram: http://2.bp.blogspot.com/-CQucyJGm-Nw/Ta-cyJu7E0I/AAAAAAAAACs/1ARDfnqIYac/s1600/7-10.gif• Competitive vs. Non Competitive Inhibitors Diagram:

http://www.tokresource.org/tok_classes/biobiobio/biomenu/enzymes/competitive_inhibit_c_la_784.jpg • Musical Note: http://wwwcdn.net/ev/assets/images/vectors/afbig/musical-note-3-clip-art.jpg