Transcript Fundamentals of Biochemistry

Welcome AP Biology teachers
Chapter 2:
Basic Chemistry
Chapter 2, Students need to
know…
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basic chemistry: covalent vs. ionic bonds
Essential elements of life: C, H, O, N, P, S
What a valence shell is, and why it matters
Atoms with open valence shells (e.g. C,
and O) are going to be reactive
• Basic periodic trends, but focus mainly on
the essential elements of life and the “go
to” trace elements: K, Na, Ca, Mg, Fe
Important THEME
Teach the Skill
• Compound
– Two or more elements bonded together resulting
in NEW chemical properties to emerge for the
compound.
– This is an example of the Emergent Properties
theme. (Fig. 2.2) An example: Water (H20) – a
stable liquid and can sometimes be used to out a
fire. Hydrogen by itself is a flammable gas; Oxygen
by itself is also a flammable gas.
IMPORTANT BIG PICTURE ITEM
– Electrons (These particles carry a negative
charge.) (They are located in the “Electron cloud”.
The cloud is created because electrons move at
the speed of light which creates a blur around the
atom.)(The electrons moving, which is called
kinetic energy, is why they are associated with
energy and batteries. It is potential energy when
they are bonded.
• The number of electrons can change. (Atoms with
different numbers of electrons than the normal amount
for that element are called Ions.)
IMPORTANT
• Energy (represented by the symbol “E”)
– Energy comes from the rapid movement of electrons
(e-) normally, but it could be neutrons too.
– Potential Energy (PE) – Energy of position. (Usually
refers to electrons “locked” in a chemical bond.)
– Kinetic Energy (KE) – Energy of movement. (Usually
refers to electrons that can move freely.)
– E levels or e- shells – Where the electrons or E is
located within an atom or molecule.(FIG. 2.7)
– Adding energy to electrons makes them move farther
out; losing energy causes them to move inward.
IMPORTANT
– Valence Shell- Where the outer most electrons
are located on an atom.
– Valence e- - Refers to the outer most electrons.
(These are the most important for chemical
bonds and properties.)
– Valence – Refers to the bonding capacity of an
atom. (Depends on the number of valence
electrons.)
Fig: 2.8
IMPORTANT and
Teach the skill
– Covalent Bonds (Fig. 2.11)
• This type is the strongest type of chemical bond.
– Results from sharing electrons between elements or molecules to fill
BOTH outer shells.
• They always create a molecule. (The size of the molecule may
differ though.)
– Two or more atoms together of any kind.
• Polar molecules (Fig. 2.12) carry an electrical charge at opposite
poles(poles refers to the “ends” of the molecule) and non-polar
molecules do not have an electrical charge
• Electronegativity
– Refers to the element’s or molecule’s DESIRE to acquire or release
electrons.
– Hydrogen atoms (LEASTelectronegative biological element)(It wants to
RELEASE e-)
– Oxygen (MOST electronegative biological element)(It wants to ACQUIRE
e-)
Oxygen is at the end
Important
– Ionic Bonds
• These are Fairly strong bonds while dry – but are weak in
water so they dissolve into ions.
• These bonds are created by swapping electrons between
elements so that each element can fill it’s outer most shell.
(Fig. 2.13)
• When dissolved in water Ions are created. (Gatorade is a ion
loaded drink.)
– Cations – possess a positive charge because it has more protons
than electrons.
– Anions – possess a negative charge because it has more electrons
than protons.
– THESE LOVE WATER. (because water is a polar molecule too.)
IMPORTANT BIG PICTURE ITEM
– Hydrogen Bonds (Fig. 2.15)
• Fairly weak bonds. (It is “like” a magnet) (A positive
Hydrogen attracted to a negative
“Substance”…USUALLY oxygen.)
• THESE ARE THE MOST IMPORTANT BIOLOGICAL
BONDS
Important and
Teach the skill
– Van der Waals Interactions
• These are temporary bonds. (Usually a fraction of a
second.)(Involves enzymes mostly.)
• These INTERACTIONS are created when electrons
clump on one side of an atom making that side
temporarily “negative” and the other side
“positive” so that charged particles can attach
momentarily and then they unclump, because
electrons are moving, and the “interaction”
disappears because of loss of the charge
AP Biology
Chapter 3:
Properties of Water
Chapter 3, students need to know…
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water is a polar molecule
water molecules “stick together” via hydrogen bonds
water has a relatively high specific heat,
Water has a high heat capacity
Why these characteristics of water matter to biological
systems
Water can ionize into H+ and OH- and this is the
chemical basis of the pH scale
The basics of the pH scale (acids vs. bases)
How to describe adhesion and cohesion,
How to identify hydrophobic & hydrophilic molecules.
IMPORTANT BIG PICTURE ITEM
• Water is a Polar Molecule
– Water’s polarity allows for it to make HYDROGEN
bonds easily which helps with nutrient transport.
– This polarity makes it possible to conduct
electricity very well. (Remember, electricity is
flowing electrons.)
– The polarity allows for a single water molecule to
bind to 4 other water molecules at a time. ( Fig.
3.2)
Important and
Teach the skill
• Cohesion
– This term refers to water molecules binding to other water
molecules.
– This property is made possible because of HYDROGEN bonds.
– This is important in the Cohesion-Tension Principle that
describes how water moves upward in plants xylem tissues by
making water “chains”. (Fig.3.3)
•
• Adhesion
– This term refers to water molecules binding to something other
than water molecules. (Fig. 3.2)
– This property is made possible because of HYDROGEN bonds.
Cohesion Visual
Important and
Teach the Skill
• Surface Tension
– This is the linking together of water molecules on
the surface of a body of water. (Fig. 3.4)
– This property is made possible because of
HYDROGEN bonds.
Surface Tension Visual
IMPORTANT BIG PICTURE ITEM
• Water helps with Temperature Regulation in organisms and on the earth.
– Water can act as a huge heat “piggy” bank. (Such as when the sunlight hits the
oceans and other water bodies and the water heats up SLOWLY as it absorbs
the light energy.)
– This property is made possible because of HYDROGEN bonds.
– It takes tremendous amounts of E to break ALL four hydrogen bonds at once
and turn liquid water to a gas.
– This is a important worldly effect as it helps to keep the temperature of earth
stable (the water absorbs the energy of sunlight, so we don’t fry, and then
releases that same energy at night, so we don’t freeze… remember that one
side of earth is always in the sun and the other side is dark so temperature is
stable.)
– Kinetic E terms associated with water.
• Heat – This measurement is the total amount of kinetic E in a substance.
• Temperature – This measurement is the intensity of all the heat in a substance as the
molecules move. (The faster they move… the hot it gets and the slower they move… the
colder it gets.)
IMPORTANT
• Specific Heat
– This measurement is the amount of heat required to raise
or lower 1g of a substance 1⁰ Celsius.
– The specific heat of water = 1 Calorie = 4.2 Joules.
• Water requires a huge amount of E to raise 1 gram of it 1⁰Celcius.
(1 gram = 1 cm³)
• The HYDROGEN bonds prevent kinetic E from increasing. (Need to
break 4 at a single time!)
• Water vs. Steel (Steel has a very low specific heat and that is why it
gets hot QUICKLY.)
– Think of it as the ability to RESIST a change in temperature.
– The fact that humans and other organism are mostly
water, this keeps us from burning up in the sunlight
literally.
IMPORTANT BIG PICTURE ITEM
• Evaporative Cooling
– Putting heat E into water, causing the water to
evaporate and carry the heat E away from the
body thus providing a cooling of the organism to
occur as the E leaves.
– Wind increases the effect of cooling by carrying
the water vapor away from the body. Humidity,
water vapor in the air, decreases the effect
because water can’t evaporate into the air as it is
already full of water vapor.
Evaporative Cooling Demo
Important Terms
• Water is the Universal Solvent
– Solvent – Liquid that is doing the dissolving of
another substance.
– Solute – Substance being dissolved in the solute.
– Solution – Substance possessing equal
distribution of material. (Kool-aid is a good
example.)
Important Terms
• Hydrophobic “hydro” means water; “phobic”
means fear of
– Water cannot attach to the substance because the
substance is non-polar.
– The substance “hates” water’s polarity.
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• Hydrophilic “philic” means love of
– Water can attach to the substance because the
substance is polar.
– The substance “loves” water’s polarity.
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Important Terms
• WET” Chemistry Terminology
– Mole (mol)
• Refers to a measurement of molecules that is relative to its
molecular weight.
• Avogadro’s Number 6.02 x 10²³
– # of molecules of that particular substance present in a 1 mole.
• Find the molecular weight of a molecule using the Periodic
Table and then weigh out that many grams of the substance
and that amount is equal to 1 mole. (Sucrose = 342 so I need
342 grams)
– Molarity
• Term for telling how many moles of a substance are
dissolved in a solution. (usually water)
AP Biology
Chapter 4:
Properties of Carbon
Chapter 4, students need to know…
• Carbon is tetravalent, and thus lends itself to a variety of
functional molecules.
• Most biologically important molecules are macromolecules
• Macromolecules are polymers comprised of monomers
• Polymers are formed by dehydration synthesis
• Polymers are broken down by hydrolysis
• How to recognize the “Big 6” Functional groups.
– The first three have O, and H in some form
– The other three are stand alones with S, N, or P in the
functional group.
– The Essential elements of life are C, H, O, N, P, S…this is
not rocket science.
IMPORTANT BIG PICTURE ITEM
• Carbon’s e- configuration (Figs. 4.3 and 4.4)
– Carbon has versatility in four directions because of
its Tetravalence. (Tetra means “four”)
– The tetravalence allows carbon to act like an
intersection in the building of an organic
molecules.
– Covalent Bonding Capabilities of Carbon
• Single Bond between Carbon atoms.(shown as: C-C)
• Double Bond between Carbon atoms. (shown as: C=C)
• Triple Bond between Carbon atoms. (shown as: C=C)
LE 4-3
Molecular
Structural
Ball-and-Stick
Space-Filling
Formula
Formula
Model
Model
Methane
Ethane
Ethene (ethylene)
IMPORTANT BIG PICTURE ITEM
• Hydrocarbons
– Molecules containing mostly Carbon and Hydrogen.
– Most hydrocarbons are Energy Sources. (Some
examples are: Fossil fuels, Oils, And Fats)
– Hydrocarbons are important parts of cell membranes.
(The tails of phospholipids)(Fig. 5.13 on page 76)
– All hydrocarbons are extremely hydrophobic because
the nonpolar molecules. (Hates water’s polarity.)
Carbohydrates
Hydrocarbon tails
Important and
Teach the Skill
• Isomers
– These are molecules with the same molecular formula but
different molecular structures.
– Three types of isomers exist (Fig.4.7)
• Structural Isomers – Same composition but have “different
shapes”.
• Geometric Isomers – Change is centered “around a central double
bond”.
• Enantiomers – These are “mirror images of each other”, like your
hands.
– To types exist: Right orientation (D) and left orientation (L).
– They will have very different properties (such as Fig.4.8) and
Thalidomide.
• Example of Emergent Properties and Structure = Function themes.
LE 4-7
Structural isomers differ in covalent partners, as shown in this
example of two isomers of pentane.
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
Geometric isomers differ in arrangement about a double bond. In
these diagrams, X represents an atom or group of atoms attached to a
double-bonded carbon.
L
isomer
D isomer
Enantiomers differ in spatial arrangement around an asymmetric
carbon, resulting in molecules that are mirror images, like left and
right hands. The two isomers are designated the L and D isomers
from the Latin for left and right (levo and dextro). Enantiomers
cannot be superimposed on each other.
Ryan’s Objectives
• Discuss the importance of carbon, the “big 6”
functional groups, monomers vs. polymers
and dehydration synthesis vs. hydrolysis
(notice the importance of water here)
IMPORTANT BIG PICTURE ITEM
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Functional Groups Associated with Organic Molecules (Fig.4.9 and 4.10)
– These are the sites of most organic molecules chemical reactions or properties. (They have a
function to do.)
– Example of Structure = Function theme.
– Hydroxyl s (-OH)
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This group allows molecules to act as an alcohol or polar molecule.
Name usually ends with “ol”.
– Carbonyls (Only has one double bonded oxygen.) (It takes ONE stroke to make a lower case
“n”.)
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Aldehydes (A is at one end of the alphabet.)(Carbonyl is located on the end of the molecule.)
Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.)
– Carboxyl (Has two oxygens…one double bonded and one singled.)(It takes TWO strokes to
make an “x”)
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These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too.
– Amine (Contains Nitrogen)
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Can act as bases by picking up free H+.
– Sulfhydrls (Contains Sulfur)
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Sulfur can make Di-Sulfide bridges for “pockets” in protein formation .(Fig. 5.20 on Pg. 83)
– Phosphate ( Contains Phosphorus)
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These molecules are usually involved in E Transfers. (ATP) Also acts like an Anion.(negative)
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
AP Biology
Chapter 5:
Macromolecules
IMPORTANT and
Teach the Skill
• Macromolecules – “Macro” means “large”
– Polymers “poly” means many; “mer” means unit.
• These are formed from individual units called monomers “Building Blocks”.
• Monomers are linked together by covalent bonds. Organisms need these to
stay intact so the strongest type of bond is used.
• These are another example of the theme: Structure = Function.
– Macromolecules are formed by Dehydration or Condensation
Reactions. (Fig. 5.2)
• Hydroxyl and Hydrogen must be aligned properly to produce water.
• This orientation of molecules and making of a bond requires E.
• Enzymes help speed up the rate of the reaction.
– Macromolecules are broken apart into individual monomers by
Hydrolysis reaction. “lysis” means to split.
• This process Releases E in the bond breakage.
• The process needs water (hydroxyl and hydrogen) to fill the open bonds on the
monomers.
• Enzymes speed up the rate of the reaction here too.
Chapter 5, students need to
know…
• This is a monster chapter. I divide it up into
the energy molecules and the structural
molecules.
• Part 1: Carbohydrates:
– CH2O are primarily energy and structure
molecules
– Glucose is the “king of the monosacchrides”
– Recognize the structure and know the function of
the polysaccharides…
• Amylose, Glycogen, Cellulose, and Chitin
– How the strucutre of these molecules relates to
their function
Carbohydrates:IMPORTANT
– The chemical composition is: Carbon = Oxygen; 2x
as many hydrogen also present.
– The names usually end with “ose”. Such as
Fructose, Glucose, Sucrose.
– These are primary E sources for cells.
Carbohydrates
See the Carbonyls and Hydroxides?
Chapter 5, students need to
know…
• Part 2: Lipids
• Lipids are a diverse set of molecules, all of
which are hydrophobic
• The difference between saturated and
unsaturated fats
• How to recognize a steroid
• That chloresterol is similar to a steroid
• Phospholipids are ambiphatic molecules, and
they are the primary component of cell
membranes
Lipids: IMPORTANT
– These macromolecules are fats, oils, waxes, and steroids.
– Most lipids are hydrophobic molecules. “Hydro” means
“water”; “phobic” means “fear of”.
– Lipids are mainly composed of Hydrocarbons (All the
Hydrogen means lipids have 2x The E of Carbs.)
– Two Main parts (Fig.5.11)
• Fatty Acid (Hydrocarbon)(Number of Carbons will be a multiple of
2 if it is made by living cells)
• 3 Carbon Glycerol molecule (alcohol) to hold the whole molecule
together.
• Lipids use a covalent bond called an Ester Linkage to hold the fatty
acid and glycerol together.
• An Ester linkage is a Carboxyl of the Fatty Acid paired
with a hydroxyl of the glycerol molecule
LE 5-11b
Ester linkage
Fat molecule (triacylglycerol)
IMPORTANT
• Steroids, Hormones, and Cholesterol
– A steroid has 4 carbon rings with the top ring looking like a
house.
– What makes them different are the attached functional
groups. These functional groups help determine the function
of the steroid.
Steroid Structure
Chapter 5, students need to
know…
• Part 4a: Proteins:
• Proteins may be the most important of the
macromolecules
• Proteins are usually pictured as purple images in
text books
• Proteins have a variety of structural and
biochemical roles in cells.
• Perhaps the most important roles of proteins
include enzymes, channel proteins and proton
pumps, communication devices across the cell
membrane and structural components of cells.
Proteins:Important
• Proteins (A. K.A. Polypeptides) and Enzymes
(Enzymes are a TYPE of protein.)
– Proteins make up greater than 50% of an organisms
dry weight.
– This is another important example of the theme:
Structure = Function. (These are very large 3-D
Molecules.)
– The monomer “building blocks” are Amino Acids
(There are 20different Amino Acids that can be
involved in making proteins. Proteins and enzymes
usually have hundreds of Amino acids in their
structure.)
Important
– Amino Acids have 4 different parts to them:
• Carboxyl end (COOH) – This part acts as the acid because it can give off the
hydrogen.
• Amine end (NH2) – The end can act as a base by accepting a third hydrogen.
• Alpha (α) Carbon – This is the central Carbon that holds the whole molecule
together.
• R group (This is the most important part as it gives each amino acid its
distinctly different property. Notice all 20 amino acids have a different R
group.) (Fig. 5.17)
– Individual Amino Acids (monomers) are bonded together by a peptide
bond. An amine end of one amino acid is positioned to combine with
a hydroxyl of the Carboxyl of the second amino acid. The open bonds
left behind by removing to make water allows for a bond between the
carbon and nitrogen to be created. When we put many amino acids
together, we get a POLYPEPTIDE or protein.
LE 5-UN78
a carbon
Amino
group
Carboxyl
group
IMPORTANT BIG PICTURE ITEM
– Arrangement and Quantity of Amino acids affect the
structure and function of that protein or enzyme.
(Structure = Function) (Fig. 5.20)
• Primary Structure (Represented by the symbol - 1’ )
– This refers to the sequence of bonded Amino Acids. THINK
“SEQUENCE” for Primary structure.
– Fredrick Sanger (in 1948) discovered the first protein Amino Acid
sequence. It was for insulin.
– Primary Sequence is REALLY IMPORTANT; just look at the
difference between Sickle-Cell Disease and normal red blood
cells. Just changing the SIXTH amino acid in the primary sequence
creates this horrible disease. The easy way to remember that it is
the SIXTH amino acid that changed, remember the number of the
devil 666. Bad number = bad disease. (Fig. 5.21)
Fig: 5.20 – Insulin 1’ sequence
IMPORTANT and
Teach the Skill
• Secondary Structure (2’ )
– HYDROGEN bonds allow for overlapping and coiling to occur in
the “folding” of the protein into that 3-D shape. All proteins must
be “folded” in order to work. THINK “FOLDS AND COILS” for
secondary structure.
– Coiling – Is referred to as an Alpha (α) helix.
– Overlapping – Is referred to as a Beta (β) pleat sheets.
• Tertiary Structure (3’ ) (“ Tert” means “third”)
– Di-sulfide bridges form Hydrophobic “pockets” to keep some
Amino Acids away from water. It keeps the hydrophobic ones
away from water.
– To make the Di-Sulfide bridge the Amino Acid Cystein is needed.
• THINK “DI-SULFIDE POCKETS” for Tertiary
structure.
2’ structure
3’ Structure
Chapter 5, students need to
know…
• Part 3: Nucleic Acids
• That nucleic acids exist and they will be
the focus of an entire unit later this fall!
Nucleic Acids: IMPORTANT
• Nucleic Acids
– Monomers are called Nucleotides
– Polymers are called DNA or RNA- It depends on the 5
Carbon sugar present in the monomer.
– These are the source of genes and hereditary
information primarily.
– Two Types (Fig. 5.26)
• DNA – This polymer is the “Master Million Dollar Blueprint”.
– It is kept “safe” in the nucleus. (Nucleus is like a vault to keep the
DNA in.)
• RNA – This polymer is like a “cheap 10 cent copy” of the
“Master Million Dollar Blueprint”. It is disposable/recyclable.
It makes messenger RNA and other RNA molecules.
Important
– Pyrimidines ( C, T,U )
• Big name small molecule. (These have 1 Carbon ring in the
Nitrogen base.)
• “Counting steps Takes you Up the Pyramid” is the easy way to
remember them.
– Purines ( A, G,)
• Small name big molecule. (These have 2 Carbon rings in the
Nitrogen base.)
• “Alabama is Purely Greater than Auburn” or “Auburn is Purely
Greater than Alabama” is an easy way to remember. It just
depends on who you like more.
– It is Always a pyrimidine paired with a purine.
– Individual nucleotides joined by a Phosphodiester bond.
The phosphate of one nucleotide is joined with the 5
Carbon Sugar of the previous nucleotide.
Fig: 5.26
IMPORTANT BIG PICTURE ITEM
– THE SEQUENCE DETERMINES WHAT PROTEIN OR
ENZYME IS MADE
• Structure = Function and Emergent Properties
• That is why it is the “BLUEPRINT”.
•
• Genes and Evolution
– The more Nucleotide sequence “genes” in common;
the more closely related the organisms are.
– The fewer Nucleotide sequence “genes” in common:
the more distantly related they are.
AP BIOLOGY
Chapter 8:
Metabolism and Enzymes
Chapters 5 & 8, students need to
know…
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Part 4b:Proteins Continued
How to recognize primary through quaternary structure
The bonds that hold each level of organization together
Enzymes are the chemical gate keepers of a cell’s metabolism
Enzymes are substrate specific
Enzymes have an active site, a place where substrates are “worked on”
Enzymes merely speed up reactions, they do not add energy to a
system
Enzymes are not consumed by the reactions they facilitate, therefore a
little enzyme goes a long way
Enzymes, like all proteins, are influenced by environmental conditions
like temperature, pH, and salinity. All enzymes have an optimal set of
environmental conditions
Enzymes traditionally end in “ase”, and their name describes their
function.
They will encounter dozens of enzymes over the course of AP Biology.
IMPORTANT BIG PICTURE ITEM
• Metabolism
– The sum of all the chemical reactions occurring in an organism.
– The collective process has two separate phases.
• Catabolism – This refers to the breaking down of a molecule.
– This process releases “potential” E found in the chemical bond between
monomers.
– This is an exergonic reaction because it releases heat to the environment
– Think Catastrophe; breaking up things.
• Anabolism –This is the assembly of molecules.
– This process requires “Kinetic” E to position molecules in away so as to create
a chemical bond between monomers.
– This is an endergonic reaction because it absorbs energy from the
environment.
– Think Anabolic steroids; these BUILD muscle.
• This is a great example of E Coupling – two different
processes united by common energy
IMPORTANT BIG PICTURE ITEM
• Thermodynamics
– The study of Heat E (Thermo) and its properties (dynamics).
– First Law of Thermodynamics (Also called the Principle of the
Conservation of E)
• E cannot be created nor destroyed ONLY transformed or transferred.
– Second Law of Thermodynamics
• Every E transfer increases the entropy of the universe.
– Entropy- means disorder; unable to do work because it is in a LOW state of
order
• Sunlight(high quality E) going in and heat (low quality E)coming out; it
can’t do work
• Conception to birth to death is how life relates to second law
– You are at your most organized state as a single cell; as you “progress” you go
move toward a state of entropy (death).
•
Important
• Free E (represented as “G”)( Fig. 8.6)
– It is referred to as “free” because E is available to
perform work. (Mainly making ATP or GTP in a cell.)
– G=H-TS (This is the formula for calculating Free E.)
• G- Free E (This amount goes from positive to negative as
catabolism of food occurs.)
• H- Total E in the system. (Starts large but becomes smaller as
food is broken down.)
• T- Temperature constant (Measured in Kelvin, ⁰C +273.)
• S- Amount of Entropy (Starts at 0 but becomes larger as the
reaction continues to produce heat and the highly organized
food molecules are broken apart more and more.)
IMPORTANT BIG PICTURE ITEM
– If ΔG is negative, then there is E available “free”
to perform work. (It is Spontaneous.)(It is
Exergonic.)
• This is the result of Cellular Respiration and Digestion.
(Catabolic processes release free E.)
– If ΔG is positive, then there is E that is not
available because it is “locked up” and can NOT
perform work. (It is Non-Spontaneous.)(It is
Endergonic.)
• Photosynthesis is a good example (Anabolic processes
store free E.)
Important
• ATP (Adenosine Tri-Phosphate)(Fig: 8.8)
– Made from Ribose sugar and the nitrogen base Adenine.
– Has 3 NEGATIVE phosphates linked together which makes it
HIGHLY unstable like a “COMPRESSED SPRING”. Unstable, means
it has the capacity do perform work remember.
– ATP converting to ADP has a ΔG = -13J ; ADP being converted to
ATP has a ΔG = 13J (The energy needed to make this bond
comes from the “free” e in our food as it is broken down.)(ADP
is recycled back to ATP.)
• D. Phosphorylation (Fig: 8.11)
• The attaching of an unstable phosphorus ion to another molecule to
make it unstable and thereby able to perform work. (Take the
phosphorus off and it quits working.)
•
Potential Energy vs. Kinetic Energy
Ryan’s Objectives
• 3) Teach the essential role of enzymes as
biological catalysts.
How? Perform AP Lab 2: Enzyme Catalysis.
Options include: the College Board’s published
AP Lab 2, using probe ware and Oxygen or
pressure sensors, or using Hudson Alpha’s
cholinesterase lab
IMPORTANT
• Enzymes
– These molecules are Biological Catalysts.
• Proteins that speed up and control the rate of a chemical reaction.
• THEY ARE RECYCLED; THEY ARE NOT CONSUMED BY THE
REACTION.
• Enzymes are Selective in what they will work with. We used
to say they had a “lock and key fit” (old term); we now say
it “fits like a glove or has an induced fit”. (new term)
• This is like putting on a latex glove… it stretches to conform to the
shape of your hand.
• Enzyme names usually end with “ase”.
•
IMPORTANT BIG PICTURE ITEM
• Free E of Activation (Fig: 8.15)
• This refers to the Free E used to start a chemical reaction in
motion. (Essentially is the energy for getting the molecules
moving and positioned so that it is possible to combine or
be torn apart.)
• The energy of activation is lowered by the action of
enzymes. (Enzymes reduce by GRABBING the molecule and
positioning it correctly… we don’t have to WAIT for nature
to do it.)
• Enzymes also replace the need for heat in most chemical
reactions (remember heat can make molecules move
faster) so that organisms don’t burn up during metabolism
LE 8-15
Free energy
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
Course of
reaction
with enzyme
DG is unaffected
by enzyme
Products
Progress of the reaction
IMPORTANT BIG PICTURE ITEM
• Factors that can affect enzymes ability to work optimally.
(“optimal” means “best” or “Fastest”)
• Temperature – freeze/cold (cold things don’t move quickly)
or Heat causing it to Denature (melt).
• pH of the environment
• Salt concentrations
• The Optimal Conditions for most human enzymes:
• 98.6˚F (35 - 40⁰C)
• pH usually between 6 – 8 (The human body’s pH of blood is an
average of 7.4.)
• Remember, this is an unstable (dynamic) environment. There is an
upper limit and a lower limit for enzymes. Beyond the limits, bad
things begin to happen. So it is basically, trying to stay between the
limits. The limits of “life”.
IMPORTANT and
Teach the Skill
• Inhibitors
• The name implies that these molecules negatively affect an
enzymes ability to work optimally. These slow down or stop
the rate of the chemical reaction.
• Two types of Inhibitors exist, based on the location of the
enzyme that is affected: (Fig: 8.19)
• Competitive- These molecules compete for the active site. (This is
because of similar shape.)
– These molecules slow down the reaction rate. (These molecules will be
removed.)
• Non-competitive –These molecules attach somewhere other than the
active site causing the shape of the active site to change so the
substrate can’t fit into it.
– These molecules cause the reaction to stop completely. (These molecules may
affect the enzyme permanently or maybe temporarily in the case of an
Allosteric connection.)
LE 8-19
A substrate can
bind normally to the
active site of an
enzyme.
Substrate
Active site
Enzyme
Normal binding
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Competitive
inhibitor
Competitive inhibition
A noncompetitive
inhibitor binds to the
enzyme away from the
active site, altering the
conformation of the
enzyme so that its
active site no longer
functions.
Noncompetitive inhibitor
Noncompetitive inhibition
IMPORTANT BIG PICTURE ITEM
• Feedback Inhibition (Fig: 8.21)
– A product IN EXCESS shuts down the reaction that
is taking place at an earlier point in the pathway.
– Prevents “waste” of precious materials and energy
by not making more of what is not needed at that
time.
LE 8-21
Initial substrate
(threonine)
Active site
available
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 can’t
bind
Intermediate B
theonine
pathway off
Enzyme 3
Isoleucine
binds to
allosteric
site
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)