Chemistry, Biomolecules, and Enzymes

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Chemistry, Biomolecules, and Enzymes

• Table 3

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Menu
Denotes a Review Song!

• Basic Chemistry
• Elements and the Periodic 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

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Elements and the Periodic Table
Element Name

• 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

Atomic Number
Chemical Symbol
Atomic Mass, Mass Number would be 23
Structure of an Atom
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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

Isotopes
Elements/Table
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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

Covalent Bonds
Atomic Structure
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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
Isotopes
Covalent (cont.)
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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 d (slight
  positive charge), and one a d- (slight negative
  charge)

Covalent Bonds
Ionic Bonds
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Ionic Bonds/ Overview

• Overview of Bonding

• 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,
  dont consist of molecules, form a crystal with a
  definite ratio of atoms

Click to start video
Covalent Bonds
Hydrogen Bonds
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Hydrogen Bonds
Quick Review of Bonding Time for a Song!

• 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

Ionic Bonds
Chemical Reactions
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Chemical Reactions
Equilibrium Diagram

• 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

Hydrogen Bonds
Properties of H2O
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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? 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

Chemical Reactions
Lipids
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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
Properties of H2O
Proteins
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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?) - sequence and types of amino acids
  used in a protein
• Secondary (2?)- shape (a helix, ß- pleated
  sheet) that different sections of the protein
  strand will take based on hydrogen bonds (between
  R- groups)
• Tertiary (3?)- 3D shape of protein caused by
  hydrogen bonds and other bonds between R-groups
• Quaternary (4?)- 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

Lipids
Protein Diagrams
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Proteins (Diagrams)
Proteins
Carbohydrates
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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
Protein Diagrams
Nucleic Acids
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Nucleic Acids
Quick Review of Biomolecules Time for a Song!

• 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

Carbohydrates
Nucleic Acids (cont.)
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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

Nucleic Acids
Enzymes (General)
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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

Nucleic Acids
Diagram of Reaction
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Diagram of a Reaction
Enzymes (General)
Substrate Specificity
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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
Diagram of Reaction
Allosteric Regulation
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Allosteric Regulation

• A proteins 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

Substrate Specificity
Regulation (cont.)
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Allosteric Regulation
allosteric inhibitor
Allosteric Regulation
Inhibitors
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Inhibitors
Quick Review of Enzymes Time for a Song!

• 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

Allosteric Regulation
Credits
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Biomolecule Review Song
Back
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Chorus Carbohydrates, Nucleic Acids, Proteins,
Lipids, Are your passes To keep you working
properly These are the molecules that you
need Theres 4 types 4 types 4 types of
biomolecules you need Verse 1 Lipids theyre
your bodys fats You saw them when we dissected
cats The phosphate heads of the bilayer They sure
like to touch water Theyre on the outside of the
cell The fatty acid tails are protected well
Verse 2 Proteins are the building blocks Of your
bodys many parts Theyve got carboxyl and amino
groups And 20 possible R groups too If amino
acids make a chain Primary structure is its
name Secondary they fold up Tertiary is a 3D
clump Quaternary they join together To build the
final protein structure Verse 3 Mono and
disaccharrides Are carbohydrates in disguise They
store short term energy From foods that are very
sugary Nucleic Acids have a phosphate 5 carbon
sugar and nitrogen base They make up your DNA ATP
and RNA Theyve got two strands antiparallel And
carry genetic info as well
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Enzyme Review Song
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Chorus Enzymes They can catalyze Chemical
reactions When they bind at their active site And
substrates Have a specific shape For the enzyme
That fits into them the right way Verse
1 Activation energy a reaction needs To start
forcefully It forms a barrier of energy
required To break the bonds that hold reactants
together But then the enzyme It comes just in
time And saves the day It lowers the barrier To
reach the transition state Reactants
unstable Reaction underway
Verse 2 Enzyme inhibitors They attempt to
block The enzyme-substrate lock Some compete
directly And some do not With the enzyme that
they want to stop Enzymes they regulate Inhibit
or activate Allosterically They can change the
shape Of a protein so that it may Stabilize its
active sites Or just inactivate
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Bonding Review Song
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Verse Just an ionic bond Transfer of
electrons It lets atoms fill Those last valence
spots Electronegativity To the higher one
electrons flee Ionic bonds oh they can
give Metallic properties And then theres
covalent bonds They can share electrons They make
non-metals strong To last on and on and on and
on Some bonds are polar Electrons shared
unequally Due to different Electronegativities
Hydrogen bonds They are weak one-on-one But
together They are strong! Chorus Dont stop
bonding Hold on to those electrons To keep that
molecule Holding strong Ionic, Covalent And
Hydrogen bonding they make Molecules stay In
their place
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Credits

• Atom Cover Art http//www.presentermedia.com/file
  s/clipart/00001000/1474
• Structure of a Carbon Atom http//www.universetod
  ay.com/wp-content/uploads/2010/02/c-atom_e1.gif
• Helium Isotopes http//www.green-planet-solar-ene
  rgy.com/images/helium-isotopes-5-to-8.gif
• Covalent Bond Video http//www.youtube.com/watch?
  v1wpDicW_MQQ
• Picture of Water Molecule http//media.wiley.com/
  Lux/33/168033.image0.jpg
• Electronegativity Video http//www.youtube.com/wa
  tch?vKj3o0XvhVqQ
• Hydrogen Bond Diagram http//academic.brooklyn.cu
  ny.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/mo
  lvis/workshop/imgs/protein-structure2.png
• Nucleotide Diagram http//www.buzzle.com/img/arti
  cleImages/387160-1237-22.jpg
• Amylose Diagram http//www.mansfield.ohio-state.e
  du/sabedon/071amylo.gif
• Antiparallel DNA Diagram http//www.tokresource.o
  rg/tok_classes/biobiobio/biomenu/dna_structure/dsD
  NA.jpgD
• Diagram of a Reaction http//www4.nau.edu/meteori
  te/Meteorite/Images/activation-energy.png
• Enzyme-Substrate Video http//www.youtube.com/wat
  ch?vV4OPO6JQLO
• Allosteric Regulation Diagram http//2.bp.blogspo
  t.com/-CQucyJGm-Nw/Ta-cyJu7E0I/AAAAAAAAACs/1ARDfnq
  IYac/s1600/7-10.gif
• Competitive vs. Non Competitive Inhibitors
  Diagram http//www.tokresource.org/tok_classes/bi
  obiobio/biomenu/enzymes/competitive_inhibit_c_la_7
  84.jpg
• Musical Note http//wwwcdn.net/ev/assets/images/v
  ectors/afbig/musical-note-3-clip-art.jpg