Biochemistry and Enzymes
Test date:
2/3
Overview
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Atoms, elements, compounds
Bonding
Properties of Water
Solution, solvent, and solute
pH, acids, and bases
Chemical reactions
Monomer, polymer, macromolecules
Enzymes
Atoms
• An atom is the smallest basic unit of matter
– In other words, it cannot be broken down any
further without damaging it
• A period on a piece of paper would contain
millions of atoms!!!
• It would take more than one trillion years to
count the number of atoms in a grain of sand!
Parts of an atom
• Proton (+)
– Center of the atom
– More dense
– Same number of protons and electrons (electrically neutral)
• Neutron (neutral=no charge)
– Center of the atom
– More dense
• Electron (-)
– Lie outside the atom
– Never come into contact with the nucleus (electron cloud)
– Much smaller than protons and neutrons
Drawing of an atom
Atomic number and atomic mass
• Atomic number number of protons, which is
unique for every element.
– Located to the left of the symbol for most periodic
tables
– In an atom that has no charge (electrically neutral) the
number of protons is the same as electrons
– Ex: 2He has an atomic number of 2
• Atomic Mass sum of protons plus neutrons
4
– Ex: 2 He would have an atomic mass of 4
– How many neutrons does it have?
Isotopes
• An element whose atoms have a different
number of neutrons, same number of
electrons and protons
• You name them by their atomic mass, which is
the sum of neutrons, electrons, and protons
• EX: Carbon has 6 neutrons, 6 protons, and 6
electrons (Carbon12)
• Isotopes of carbon Carbon13 (7 neutrons, 6
protons, and 6 electrons) and Carbon14 (8
neutrons, 6 protons, and 6 electrons)
Element
• Two different possibilities
– A group of atoms of the same type
– One particular type of atom that cant be broken
down
– Name some elements:
• Hydrogen, oxygen, nitrogen, carbon, gold, iron, nickel,
aluminum, helium are all common elements
• If all atoms are made up of protons, neutrons,
and electrons, are all elements the same?
– If not, what makes one element different than the
other
Elements
• All elements have a different number of protons in
each atom
– For example, hydrogen atoms have only one proton,
while oxygen atoms have 8 protons
• Electrons of each atom of an element determine the
properties of that element
• The electrons move around in their “clouds” forming
energy levels
• Different energy levels can hold a different number of
electrons
• The different energy levels are sometimes called
orbitals
• Most atoms are more stable when the orbital is full
Electron clouds
• An orbital is a “shell” around the nucleus
where the electrons are traveling
• Different orbitals can hold various amounts of
electrons.
– Ex: the first shell can only hold 2 electrons, but
the second shell can hold 8
• The left-to-right sequence of elements in each
row corresponds to the sequential addition of
electrons (and protons)
Valence Electrons
• The term for the amount of electrons in the
outermost shell
• Full outer shell is going to be 8 for any
element used in this course
Elements in biology
• Of all the 91 elements that naturally occur on
earth only 25 are found in organisms
• Just 4 elements make up 96% of humans
– Carbon, oxygen, nitrogen, and hydrogen
• The other 4% comes from trace amounts of
many other elements
– Even if they are in small amounts, it is essential for
your body to have them
– Ex: Iron, Calcium, Phosphorous, Magnesium,
Potassium, Sulphur, Sodium
Compounds
• Substance made of atoms of different elements
bonded together in a very specific ratio
• Impt compounds:
– Water (H2O)
– Carbon Dioxide (CO2)
• Compounds properties are very different than
the elements they are made up of
– Ex: Hydrogen and Oxygen are both gases, but together
form a liquid at room temperature
– Ex: A diamond is pure carbon, but it is black
• Carbon is also in sugars, proteins, and almost all compounds
Ions and ionic bonding
• Ion an atom that has gained or lost an electron
– An atom cannot lose protons
• An ion is formed and is less stable than the original atom
• An ion that loses electrons becomes (+) because it has
more protons than electrons (cation)
• An ion that gains electrons becomes (-) because it has less
protons than electrons (anion)
• Ionic compounds are compounds created when both atoms
are ions (one positive and one negative)
• We have some names for this, ionic compound or salt
• To summarize, one atom gains, the other loses an electron
creating a polar compound
• Ex: NaCl (table salt)=sodium chloride
Drawing of ionic bonding
Covalent Bonding
• Some atoms do not like to gain or lose electrons easily
• Some can only bond covalently when two or more
compounds share a pair of valence electrons
• Covalent bonds are much stronger than ionic bonds
• When shared, all atoms have to have a full outer
orbital (shell)
• Some elements occur naturally this way
– Hydrogen, nitrogen, and oxygen are usually seen in pairs
that share electrons (O2, H2, and N2)
• Ex: Carbon dioxide (CO2)
Water (H2O
Types of covalent bonds
• Nonpolar covalent bondsEqual sharing of
electrons
– Single bonds-share one pair
– Double bonds-share two pairs
– Triple bonds-share three pairs
• Polar covalent bonds unequal sharing of
electrons resulting in one partial positive charge
and the other being a partial negative charge
• The type of bond is determined by the difference
in the electronegativities of the elements
involved
Drawing of covalent bonding
Structural formula
• Represented by all atoms involved in the bond
with “lines” between them
• The line is representing the bond
• Single bond= single line
• Double bond=double line
• Triple bond=triple line
• Molecular formula the formula without the
lines for bonds
Properties of Water
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Hydrogen Bonding
Adhesion
Cohesion
Surface tension
Polarity
Specific heat
Heat of vaporization
“the calorie”
Water
• H2O
• Your body has to have water:
– Gives cells structure
– Allows for transport
– All processes necessary for life take place in an aqueous
environment-water
• Why does ice float in water?
– Less dense as a solid than as a liquid-very few compounds
behave this way
• Contains hydrogen bonds
• Polar
• Opposite charges of two polar molecules can form
hydrogen bonds
Hydrogen Bonding
• An attraction between a slightly negative atom
and a slightly positive atom
• Usually forms many bonds with many of the
same type of molecule
– Ex: very many water molecules all bound
together in unison
• Very weak as individual bonds, but are very
strong as with numbers of molecules
• Why is hydrogen bonding important:
– Adhesion, cohesion, surface tension,
Drawings of a water molecule
Polarity and strength of bonds
Most polar
Weakest
Least polar
Strongest
Adhesion
• Comes from the word adhere to stick to
• Adhesion is the ability of water to stick to other
things
• “Trickle” on sides of water bottle
• The water is actually sticking to the sides of the
water bottle
• The reason for a meniscus inside a test tube or
graduated cylinder
• This is very important for plants
• Celery
Cohesion
• Comes from the latin prefix “co” which means
together
• The ability for water molecules to stick to each
other using hydrogen bonds
• Water “beading” up on your windshield when it
rains or when it has been washed
• Reason for surface tension top layer of water
that is “harder” than the underneath layers
• Why it hurts when you dive into water
• “Jesus Lizard”
Dehydration Synthesis
• De-Hydra-tion
• Synthesis
• Chemical Reaction that involves the loss of
water (water gets used up) in order to
combine two or more reactants
• Ex: Glucose and fructose can combine
together to make table sugar, the reaction
uses up water
Hydrolysis
• Hyro-Lysis
• Breaking apart chemical bonds by using water
to do so, which in turn breaks apart the water
• Salts of weak acids or bases are dissolved in
water, breaking apart the water and breaking
apart the salt
• Ex: dissolving sulfuric acid and water uses
hydrolysis, because the sulfuric acid
dissociates into hydronium and bisulfate
Dissolving in water
• Solution is what is created when one substance is
dissolved in another
• Solvent the liquid that dissolves the solid; usually water
• Solute the solid that gets dissolved
• The amount of solute that gets dissolved in a certain amount
of solvent is called the concentration of the solution
• If you are mixing Kool-Aid, and put a small amount of mix, it
will taste very weak, but as you put more mix into the
solution, it will taste more like Kool-Aid and less like water
• Biology ex: bloodplasma is 95% water, so the solvent is
water, the sugars, proteins, etc. in plasma are solutes, and
plasma is the solution
Heat and Water
• Water has a high specific heat
• Specific heatthe amount of heat that must
be absorbed or lost for 1g of that substance to
change its temperature by 1 degree celsius
• The specific heat of water is measured in
Calories
• Kilocalorie 1000 calories
• The “calories” on food packages are actually
kilocalories
Heat of Vaporization
• The amount of heat a liquid must absorb for
1g of it to be converted from the liquid to the
gaseous state
• Water has a high heat of vaporization
• Both of these properties changes weather and
climate patterns globally
• In what climate region does the temperature
change the most?
Least?
pH scale
• Stands for potential hydrogen (H+)
• A solution with pH of 0 is very acidic with a high
concentration of H+
• A solution with a pH of 14 is very basic with a low
concentration of H+
• A solution with a pH of 7 is neutral, neither basic or
acidic
• Most living organisms need to keep their pH around 7
– Exception: Azalea bush needs a pH of around 4.5
• Buffers compound that can bind to an H+ ion when
the ion concentration increases, and can release an H+
ion when the H+ concentration decreases
– In simple terms, it keeps the pH around 7
– Normal pH of blood is around 7.4, anything above 7.8 and
below 6.8, causes fatalities
Drawing of pH scale
Organic vs inorganic
• Organic compounds are those that contain
Carbon
– CO2
• Inorganic compounds are those that do NOT
contain carbon
– H2O
Hydrophobic vs Hydrophillic
• Hydrophobic molecules that are “afraid” of
water, meaning that they do not form bonds with
water, mix with, or dissolve in water
– Usually going to be nonpolar substances
• Hydrophillic molecules that “love” or have an
affinity for water, meaning that they will form
bonds with, mix with, and dissolve in water
– Usually going to be polar substances
What type of stains are better for
clothing?
• Hydrophillic vs hydrophibic?
• Water based or carbon based?
• This is the very basis for how soaps and
detergents work.
• Water-induced clumping of hydrophobic
molecules
– What color is carbon?
– When you burn wood, what color are the ashes?
– If you burnt an orange, what color would the
ashes be?
– If you burned a person, what color would the
ashes be?
Carbon-based molecules
• Carbon is the basis for all life, anything living is
made up of carbon
• People say that anything living makes good
compost, because it breaks down into carbon,
which is the basis for soil, hence the black color
• Carbon is so important because of its atomic
structure
– Has four valence electrons, therefore, it can form covalent
bonds with up to four other molecules at once
– Draw picture
– Organic chemistry the study of carbon compounds
Types of carbon formations
• Ring
• Branched
• Straight
Important Vocab
• Monomer: subunits of a complex molecule
– One
– “What can the macromolecule be broken down
into?”
• Polymer:
– Many monomers bound together in a chain or
strand
– Can be all the same monomer (starch) or all be
different monomers (proteins)
– “If you put the monomers together, what do you
get?”
Picture of monomer and polymer
Four Macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids
Carbohydrates
• Molecules composed of carbon, hydrogen, and
oxygen
• Can be broken down into starches, and starches into
sugars
• Carbohydrates get broken down into useable
energy=ATP
• Basic carbohydrates are called monosaccharides=one
sugar
• Simple sugars usually have five or six carbons in a chain
– Ex: fructose, glucose
• These simple sugars can bind together in repeating
units creating a polysaccharide=many sugars
– Ex: table sugar sucrose=glucose + fructose
Complex carbohydrates
• Starch
– Branched chains of glucose
– Can be broken down into simple glucose sugars and used
for energy by plants and animals
• Glycogen
– Used and stored only in animal cells
– Highly branched
• Cellulose
– Used by only plants, animals cannot break down cellulose
– This is why it is stored as “butt dimples” in humans
– Makes up the cell wall in plants and helps plants stand up
by themselves
• Ex: celery
Uses for carbohydrates
• In animals, provide energy (short term, fast
acting)
• In plants, carbs are the product of
photosynthesis
• Foods
– Corn, potatoes, rice, pasta, any other starch
• Real life application
– Why does the food pyramid suggest that we eat
more carbs than any other type of food?
Drawing of carbohydrates
Lipids
• Non-polar molecules, what does that mean?
• Fats, oils, cholesterols, and steroids
• Some lipids can be broken down into usable
energy for cells, others help out with the
structure of the cell (later chapter)
• Fats and oils actually contain much more
energy than carbohydrates (long lasting, but
harder to break down)
– Animal fats meat and butter
– Plant fats vegetable and peanut oil
Structure of lipids
• Contain repeating units of three fatty acids bonded to
a glycerol, which is called a triglyceride
• Saturated fatty acids no double bonds
– Not so good fats
– Usually true animal fats such as lard and butter
– Solid at room temperature
• Unsaturated fatty acids contain at least one double
bond
– Better fats for you health wise
– Usually in the form of oils (double bond makes them
liquid)
Uses for lipids
• Function:
• Cell membrane=phospholipids
• Insulation
• Organ protection
• Is bad if your body has too much, but it is
essential for life
– A lot of steroid based hormones such as estrogen and
testosterone are made from cholesterol
– Also is part of the cell membrane, and helps it be
more fluid
– Real life application when you have a fever, it is
your bodies way of “melting” the cholesterol to allow
the pathogens to escape out the cell membrane
Steroids
• Cholesterol
– Is bad if your body has too much, but it is essential
for life
– A lot of steroid based hormones such as estrogen and
testosterone are made from cholesterol
– Also is part of the cell membrane, and helps it be
more fluid
– Real life application when you have a fever, it is
your bodies way of “melting” the cholesterol to allow
the pathogens to escape out the cell membrane
• Hormones such as estrogen, progesterone, and
testosterone are also considered steroids
Drawing of fatty acid chains
Nucleic Acids
• Polymers that are made up of monomers of
nucleotides
• Basis for DNA and RNA
• Instructions for building proteins
• Nucleotide sugar, phosphate group, and a
nitrogenous base
• Unlike all the others who have many functions,
nucleic acids only have one, to make proteins
• You will learn a lot more about nucleic acids later
in the year
Proteins
• NOT repeating units, instead they vary
depending on structure and function
• A protein is a polymer made up of monomers
called amino acids
• Amino acids are molecules that contain carbon,
hydrogen, nitrogen, oxygen, and sometimes
sulfur
• There are 20 different amino acids that can
combine together in any order to create millions
of different proteins
• Your body can make 12 of these naturally, the
others we have to eat
Structure of amino acids
• All amino acids have similar structure
– Carbon bonded to
• Hydrogen atom
• Amino group
• Carboxyl group
• Amino acids differ only in their side group
• Amino acids form covalent bonds with each called
peptide bonds
• Many amino acids bond together forming
polypeptides
• More than one peptide bound together is called a
protein
Important info about proteins
• Proteins differ in the particular amino acids
used to make them
• Also they differ in the number of amino acids
• These two things determine the structure and
function of the protein
• Functions of proteins:
– Cellular transport into and out of the cell
– Cellular transport from organelle to organelle
– Helps make DNA and genes
– Enzymes are a specific type of protein that has
many functions
Four levels of protein structure
• Proteins do NOT exist in straight chains, instead they
coil and fold into very complex spatial confirmations
• Primary-simple chain
• Secondary-alpha helix and beta pleated sheet
• Tertiary-alpha helix and beta pleated sheet together
after folding occurs
• Quaternary-four sections of tertiary level proteins all
bound together
Protein Folding
• Chaperonins molecules that assist the
protein in folding itself
– They basically make sure the structure is not
damaged by outside forces and molecules
• Takes several steps that scientists do NOT
know all of at this point in time
• X-ray crystallography is the best method for
examining the final three dimensional
structure of a protein
Pics of levels of protein structure
Summarize
Chemical Reactions
• Change substances by breaking and reforming
chemical bonds
– Burning wood
• Physical reactions, just alters the state of the
chemical involved
– Ice melting
• Important vocab:
– Reactant, Product, bond energy, activation energy,
equilibrium, exothermic, and endothermic
• Important tools
– Balancing equations
Basics of chemical reactions
• Reactants what goes into the reaction
– “ingredients”
– What gets broken down
• Products what comes out of the reaction
– Final outcome
– What gets reformed
Bond energy
• Bond energy is the amount of energy needed to
break a bond between two atoms
• This is different and unique for each type of
atom
• A certain amount of energy is needed to break
bonds between two oxygen atoms
• A certain amount of energy is needed to break
hydrogen bonds in water
• Energy is also needed to form a bond
• The energy needed to form a bond is equal to
the amount of energy needed
Chemical Equilibrium
• Some reactions continue until all the reactants
are used up, and you are left with only product
• However, other reactions can also work in
reverse, and turn the product back into reactant
• Actually what happens is that reactants are
being turned into products at the same rate as
products are turning into reactants
• We call this chemical equilibrium= state of
equality (amount of reactants=amount of
products; 50% of each)
Energy in chemical reactions
• All chemical reactions involve changes in energy
– Energy is never created or destroyed
• Energy that is added to the reaction breaks down
their chemical bonds
– Can be in the form of heating the reaction up, cooling it
down
• Energy is released at the end of the reaction when the
product is formed
– Can be heat, steam, cold, etc.
• All chemical reactions do both, it takes some energy
to start the reaction and also energy gets released
– The ratio of absorbtion vs. releasing is determined by
bond energy
Activation energy
• The amount of energy that needs to be
absorbed for the reaction to occur
– Can think of it like the energy it takes to roll a rock
up a hill, once it gets to the top, it will roll down
by itself
Exothermic
Endothermic
• Releases more energy than
it absorbs
• Products have lower bond
energy than the reactants
• The excess energy is
released as heat or light
• Ex: fireflies, squids
• Cellular respiration is an
example of an exothermic
reaction that keeps your
body warm
• EXO=Exit
• Absorbs more energy than
gets released
• Takes more energy to start
the reaction than gets
released
• Products have higher bond
energy than the reactants
• Photosynthesis is an
example of an endothermic
reaction, because it needs
sunlight to start the
reaction
• ENDO=Into
Drawings and examples
Enzymes
• Vocab:
– Enzymes
– Catalysts
– Substrates
– Active site
– Lock and key model
– Induced fit model
Catalysts
• Some reactions take a long time to absorb
enough energy to break the activation energy
threshold
• Other reactions, even after threshold has been
reached, takes a long time to form products
• Catalysts fix both problems, enzymes are used
to lower the activation energy required to start
the reaction, therefore, speeding up the reaction
Drawing
Enzyme (almost always end in “ase”)
• Catalysts for chemical reactions produced in
living organisms (known as biocatalysts)
• Specific types of proteins
• They act just like a catalyst in a chemical reaction,
they lower activation energy speeding up the
chemical reaction
• In reactions that are reversible, enzymes do not
affect chemical equilibrium
• They DO NOT change direction, only rate of
reaction
Enzymes in biology
• Involved in almost every process in living
organisms
• Help break down food (saliva)
• Build proteins
• Your body could not break down food without
the enzyme in saliva called amylase
• Still long chains of amino acids
• Function of enzyme depends on order and
structure of amino acids
Enzyme Structure
• Enzyme structure is very important because each
enzyme’s shape determines what reactants can
bind to the enzyme
• The specific reactant in which an enzyme can
bind is called its substrate
• Ex: Amylase only breaks down starch and turns it
into sugar.
– Enzyme=amylase
– Substrate=starch
– Product=sugar
How do enzymes work?
1. Enzyme is specific to certain substrate
2. Substrates bind to the enzyme at active site
3. The enzyme brings substrates together, lowers
activation energy, and weakens their bonds
4. The catalyzed reaction forms a product that is
released from the enzyme (which goes unchanged
throughout chemical reaction-gets recycled to be
used again)
Picture and Video
• http://highered.mcgrawhill.com/sites/0072495855/student_view0/ch
apter2/animation__how_enzymes_work.html
Changes in enzyme function
• All enzymes have a specific temp, pH, and concentration that they
work the best
• Temperature
– When temps are decreased, enzyme will work, but much slower
– When temps are increased, enzyme will become denatured
break down
• pH
– Increases or decreased in pH can cause the enzyme to work
slowly, or too quickly
– Also, changes in pH can cause the enzyme to become denatured
• Enzyme concentration
– All enzymes have a specific substrate/enzyme ratio in
concentration, and deviations from that ratio causes enzyme to
not work or become denatured
Lock-and-Key model
• The theory that a substrate and enzyme fit
together like a lock and key
• The fit must be perfect, and that some
substrates may fit, but if they are not perfect,
then the enzyme wont react with the
substrate
• Original accepted model until more recently
Drawing
Induced Fit
• The idea that substrates are still specific for
certain enzymes, but they do not fit perfectly
• Instead they fit good, and go through a
conformational change in order to make it fit
better
• The best analogy is like a glove, it fits, but never
fits perfectly, you have to stretch it to make it fit
better
• My analogy is like an adjustable (one size fits all)
hat
• Now more accepted than lock-and-key model
Drawing
Inhibitors
• Inhibitors do exactly as the name says, they
inhibit enzymatic activity
• In other words, they “mess up” the active site,
and prevent the substrate from binding to the
enzyme
• Many different types
– Reversible Inhibitors only change for that one time
• Competitive, uncompetitive, non-competitive, and mixed
– Irreversible inhibitors changes that enzyme forever
• Also known as suicide inhibitors
Competitive
• The inhibitor and substrate are both trying to
bind at the same time, and both cannot
• One will outcompete the other depends on
the concentration
• Can be reversible by increasing the
concentration of the substrate
• Ex: statins that lower cholesterol
Non-Competitive or Mixed
• The Inhibitor binds to the enzyme at a
different spot than the active site, and causes
the enzyme to go through a conformational
change that results in the substrate no longer
fitting/working
• Irreversible once the enzyme has been
modified, the substrate will never be able to
bind to that enzyme again
• Ex: Aspirin
Uncompetitive
• The inhibitor binds to the enzyme after the
substrate has already bound to it
• The enzyme is still going to convert the
substrate into products, but the products
cannot be released because of the inhibitor
Suicide Inhibitors
• Irreversible
• Inhibitor binds to the active site instead of the
substrate causing a permanent
conformational change to the enzyme
therefore destroying it from ever binding to
the substrate again.
• Looks just like noncompetitive
Feedback Inhibition
• The process of the body being able to selflimit itself by the use of substrates and
inhibitors
• When your body increases too much of a
substrate, inhibitors will be activated so no
more of the substrates get broken down and
vice versa
Real Life Application
• Most drugs are inhibitors
• They inhibit neurotransmitters and hormones
(substrates) from binding to specific enzymes
• They can also prevent the body from
destructive damage when the body is
attacking itself
• Suicide Inhibitor example is chemotherapywhich completely kills the cells and the
enzymes involved
Pharmaceuticals
• Asprin suicide inhibitor
• Penicillin suicide inhibitor
• ACE (angiotensin converting enzyme) Inhibitors
– Angiotensin (hormone) constricts blood vessels and
arteries causing high blood pressure and decreased
blood flow
• Naturally occurs when blood flow needs to decrease (sleep,
dehydration, bloody injury)
– ACE inhibitors prevent the body from making
angiotensin