Chemistry, Biomolecules, and
Enzymes
Table 3
Denotes a
Review
Song!
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• Basic Chemistry
– Elements and the
Periodic Table
– Structure of an Atom
– Isotopes
• Chemical Bonds
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Covalent Bonds
Ionic Bonds
Hydrogen Bonds
Chemical Reactions
• Properties of Water
• Macromolecules
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Lipids
Proteins
Carbohydrates
Nucleic Acids
• Enzymes
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General
Substrate Specificity
Allosteric Regulation
Inhibitors
• Credits
Elements and the Periodic
Element
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
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Name
Atomic
Number
Chemical
Symbol
Atomic Mass,
Mass Number
would be 23
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
Elements/Table
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Isotopes
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
Atomic Structure
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Covalent Bonds
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
Isotopes
Click to start video:
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Covalent (cont.)
Covalent Bonds
• Non-Polar- between two
atoms with the same
electronegativity,
electrons are shared
equally
Covalent Bonds
• 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)
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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/Saltsformed by ionic bonds,
don’t consist of molecules,
form a crystal with a
definite ratio of atoms
Covalent Bonds
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Overview of Bonding
Click to start video:
Hydrogen Bonds
Hydrogen Bonds
• Hydrogen Bondattraction 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
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Quick Review
of Bonding:
Time for a
Song!
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
Hydrogen Bonds
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Equilibrium Diagram
Properties of H2O
Properties of Water
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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
Chemical Reactions
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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
Properties of H2O
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Glycerol
Fatty Acid Tails
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
Lipids
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Protein Diagrams
Proteins (Diagrams)
Proteins
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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
Protein Diagrams
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Nucleic Acids
Nucleic Acids
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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
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Nucleic Acids (cont.)
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
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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
Nucleic Acids
• 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
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Diagram of Reaction
Diagram of a Reaction
Enzymes (General)
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Substrate Specificity
Substrate Specificity
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Click to start video:
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Diagram of Reaction
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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
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
Substrate Specificity
• 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
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Regulation (cont.)
Allosteric Regulation
allosteric
inhibitor
Allosteric Regulation
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Inhibitors
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
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Credits
Back
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Biomolecule Review Song
Chorus:
Carbohydrates, Nucleic Acids,
Proteins, Lipids,
Are your passes
To keep you working properly
These are the molecules that you need
There’s 4 types
4 types
4 types of biomolecules you need
Verse 1:
Lipids they’re your body’s fats
You saw them when we dissected cats
The phosphate heads of the bilayer
They sure like to touch water
They’re on the outside of the cell
The fatty acid tails are protected well
Verse 2:
Proteins are the building blocks
Of your body’s many parts
They’ve 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
They’ve got two strands antiparallel
And carry genetic info as well
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Enzyme Review Song
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
Verse:
Just an ionic bond
Transfer of electrons
It lets atoms fill
Those last valence spots
Hydrogen bonds
They are weak one-on-one
But together
They are strong!
Electronegativity
To the higher one electrons flee
Ionic bonds oh they can give
Metallic properties
Chorus:
Don’t stop bonding
Hold on to those electrons
To keep that molecule
Holding strong
And then there’s covalent bonds
They can share electrons
They make non-metals strong
To last on and on and on and on
Ionic, Covalent
And Hydrogen bonding they make
Molecules stay
In their place
Some bonds are polar
Electrons shared unequally
Due to different
Electronegativities
Credits
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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/TacyJu7E0I/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