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Biochemistry

1. Introduction to biochemistry
2. Structure and function of biomolecules
3. Enzymes
4. Closer look at the cell
Introduction to biochemistry: the
atom
Electron configuration for potassium can be written in a short
form of the Bohr diagram: K)2e)8e)8e)1e
Ion: total number of electrons is not equal to the total number of
protons
Anion: gained electrons to become stable and now negatively
charged
Cation: lost electrons becomes positively charged
Lewis diagram: valence electrons diagram
Valence electrons: number of electrons occupying the last shell
Protons and Electrons are the same as the atomic number
Neutrons: atomic mass- atomic number
Biochemistry: Radioisotopes
A radioisotope is a special type of isotope that has an unstable
nucleus.
As it breaks down in order to contain fewer neutrons during a
process called radioactive decay, it emits radiation.
The time it takes for the isotope to complete half of its decay
process is called its half-life.
The decay process occurs at a constant rate; it can act as a
clock, to help determine the age of materials.
The radiation emitted can be detected as a form of light, and
can therefore serve as a marker for the progress of biochemical
reactions.
Biochemistry: intramolecular bonds
There are three main types of intramolecular bonds:
1. Ionic bonds - one atom transfers electrons to
another atom
2. Covalent bonds - two or more non-metals share one
or more pairs of electrons.
3. Polar covalent bonds - unequal sharing of valence
electrons between atoms in the pair, with one atom
pulling harder on the electrons than the other.
Ionic bonds
When one atom transfers there electron to another
Ionic bonds usually form between metals and non-
metals. Opposite charges attract and the charge
attraction is what forms the ionic bond.
Electronegativity is a measure of an atoms ability to
attract electrons in a chemical bond.
Biochemistry: intramolecular:
Covalent bond
A covalent bond forms when two or more non-metals
share one or more pairs of electrons.
As a result, the atoms end up with a stable electron
arrangement in their outer orbit, similar to that of a
noble gas.
The simplest example of a covalent bond is between a
diatomic molecule.
Biochemistry: intramolecular: Polar
Covalent bond
It is formed when there is an unequal sharing of valence electrons
between atoms in the pair, with one atom pulling harder on the
electrons than the other.
This results in different ends of the molecule having different
electric charges.
Because this results in two poles, the molecule is said to be a
dipole, with one end being slightly positive and the other, slightly
negative.
Whichever atom pulls the hardest on the electrons will become
the slightly more negative pole (higher electronegativity), while
the other one will become more positive (lower electronegativity).
Biochemistry: intermolecular forces
London forces - Hold non-polar molecules together,
Very weak forces of attraction, Momentary dipoles are
created by the electrons contained within the
compound, which are constantly in motion.
Dipole-dipole Forces - Hold polar molecules Together,
These forces are stronger than London forces.
Hydrogen bonding - Is formed between the
electropositive hydrogen dipole and an electronegative
dipole of oxygen, chlorine, or fluorine.
Biochemical reactions
There are four main reaction types that are important in
biochemistry:
1. Hydrolysis
2. Condensation
3. Oxidation-reduction (redox)
4. Neutralization reactions
Biochemical reactions: hydrolysis
Hydrolysis: uses water to help break down
molecules
(hydro means water and lysis means to break
down).
Protein + water amino acid + amino acid
Dimethyl ether + water methanol + methanol
Biochemical reactions:
Condensation
Condensation reactions occur when two molecules
combine to form one molecule.
They are the opposite of hydrolysis reactions.
In most biochemical condensation reactions, water is produced
when two smaller molecules join to produce a larger molecule.
This is also known as dehydration synthesis because water is
removed (dehydrated) in the synthesis of the new molecule.
Amino acid + amino acid protein + water
(product is a synthsis and water)
Biochemical reactions: redox
Reduction and oxidation
LEO says GER lose electron oxidation, gain electron reduction
The process of losing electrons is called oxidation.
The process of gaining electrons is called reduction.
An electron transfer between two substances always involves a
reduction of one and an oxidation of the other, and so is
commonly called a redox reaction. (produce ATP in body)
Zn(s) + Cu2+(aq) Cu(s) + Zn2+(aq)
Notice what happens to the reactants in this equation. The zinc
atoms in solid form lose two electrons to form zinc ions in
aqueous form (Zn(s) Zn+2(aq)). Meanwhile, the copper ions
in aqueous form gain two electrons to form copper atoms in
solid form (Cu2+(aq) Cu(s)).
Biochemical reactions:
Neutralization
Neutralization reactions are the reaction of an acid and a base to produce water
and a salt.
When an acid reacts with a base, a neutralization reaction occurs because
water is produced from the H+ and OH ions in solution. For example, sodium
hydroxide (NaOH) and hydrochloric acid (HCl) react together to form the salt,
sodium chloride (NaCl), and water:
NaOH + HCl NaCl + H2O
The neutralization reaction is very important in biochemistry because it is used
to regulate the pH of the internal environment, which determines the speed
and direction of many critical biological reactions such as DNA synthesis.
One way in which organisms use the neutralization reaction to regulate internal
pH using a system of acid-base buffers- this happens by taking up excess
hydrogen or hydroxide ions, thus neutralizing excess acid or base.
Biochemical reactions:
Neutralization
Properties of Acids and Bases Pure water contains H2O molecules, as well as a tiny number of H+
and OH ions, through a natural process of ionization. H2O OH + H+ The ions in the water create
the properties of an acid and a base.
The hydrogen ion have pH values of below 7. ( increase H+ in water) have the following
characteristics of an acidic solution:
It has a sour taste.
It conducts electricity.
It turns litmus paper red.
It has a pH of below 7.
The hydroxide ion, bases have pH values of above 7 (increase OH in water) have the following
characteristics of a base:
It has a bitter taste.
It has a slippery feel.
It turns litmus paper blue.
It has a pH of above 7.
Acids are substances that, when dissolved in water, increase the concentration of the hydrogen ions.
Bases are substances that, when dissolved in water, increase the concentration of hydroxide ions.
Biochemical reactions:
Neutralization: acids and bases
Acids and bases may be classified as strong or weak, depending on the degree to

which they ionize when dissolved in water. Strong acids (for example, hydrochloric
acid, HCl)
and strong bases (for example, sodium hydroxide, NaOH) ionize completely when
dissolved in water:
HCl(aq) + H2O H3 + Cl
NaOH(aq) + OH
Weak acids (for example, acetic acid, such as vinegar, CH3COOH) and weak bases
(for
example, ammonia, NH3) ionize only partially in water:
CH3COOH(aq) + H2O CH3COO + H3O+NH3(aq) + H2O NH4 + OH
Notice that double arrows are used to represent the chemical equations of weak
acids and bases because these reactions are reversible
Lesson 2- Structure and
Function of biomolecules (functional groups)
Lesson 2- Structure and
Function of biomolecules
The functional groups are hydrophilic.
Macromolecules are large molecules made up of smaller repeating units
called Monomers.
anabolic (building-up to macromolecules using condensation, H2O
removed from reaction)
catabolic (breaking down to monomer using water, process called
hydrolysis)
The four macromolecules of life:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Lesson 2- Structure and
Function of biomolecules:
Carbohydrates
Carbohydrates used as building materials for energy,
and for cell identification and communication.
Carbohydrates are classified into three groups:
1. Monosaccharides- The most important
monosaccharides are isomers of each other: glucose,
galactose, and fructose. They all have the same
molecular formula: C6H12O6
2. Oligosaccharides -
3. Polysaccharides
.
Monosaccharides
Monosaccharides (mono- means one, and saccharide means sugar)
are simple chains that can form rings when they dissolve in water.
These sugars are distinguished from one another by the carbonyl group they
possess.
When dissolved in water, sugars with five or more carbons form ring
structures. When dry, they form linear structures.
There are two types of monosaccharide:
Aldoses- All carbons have hydroxyl groups attached, with the exception of a
carbonyl group found on the last carbon. Glucose, ribose, galactose
Ketoses- All carbons have hydroxyl groups attached, with the exception of a
carbonyl group found the second carbon. Fructose, ribulose
Molecules that contain the same atoms, but in a different order or
arrangement, are called isomers.
Oligosaccharides
Oligosaccharides (oligo- means few) contain two or
three simple sugars, attached to one another by
covalent bonds, called glycosidic linkages.
Glycosidic linkages are formed from dehydration
synthesis reactions.
These reactions form disaccharides such as lactose,
maltose, and sucrose.
Glucose + glucose maltose + water
Glucose + fructose sucrose + water
Glucose + galactose lactose + water
Polysaccharides
Polysaccharides are polymers composed of several hundred to
several thousand monosaccharide subunits, held together by
glycosidic linkages.
These molecules are very important in our diet and provide
much of natures building material.
There are four types of polysaccharides:
1. Starch
2. Glycogen
3. Cellulose
4. Chitin.
Polysaccharides: starch, glycogen
Starch is composed of amylose (with 1-4 links) and amylopectin (with 1-6 links).
It is the primary energy storage molecule for plants. Root vegetables, such as
carrots and potatoes, have an abundance of starch, which humans can digest for
energy.
Like starch, glycogen is composed of 1-4 links, and 1-6 links where it branches,
but glycogen is more branched than starch. It is the main energy storage molecule
for animals.
Glycogen regulates blood glucose levels.
As glucose increases, the liver and muscles convert excess glucose to glycogen.
Enzymes in the liver and muscles can also break glycogen molecules apart, when
glucose is required.
For example, adrenalin stimulates the breakdown of chemical bonds in a glycogen
chain for quick energy, such as that needed for an animals flight or fight
reaction when it is confronted with danger.
Polysaccharides: Cellulose, Chitin
Cellulose is composed of 1-4 links. Every other glucose subunit becomes inverted
to accommodate this link.
Unlike starch and glycogen, it is not coiled or branched. This allows cellulose to form
long chains that are tough, making it an ideal building material for plants.
For example, it is used in plant cell walls, to make them rigid and firm. Humans
cannot digest cellulose. However, it is a form of fibre.
Cellulose is the tough thread that plants use to make them rigid, and that humans
began to use long ago as a manufacturing material
Chitin is a cellulose-like polymer of N-acetylglucosamine. The monomer is a glucose
molecule with a nitrogen-containing group attached at the second carbon position.
Chitin is used by insects and crustaceans (for example, shrimp, lobster, and crabs) to
form their hard exoskeletons.
Since chitin is such a strong material, we use it to manufacture items such as surgical
thread.
Lipids
Lipids (fats) are a group of organic molecules that dissolve in oils, but not in water.
They are very efficient energy-storage molecules that yield about twice the amount of
chemical energy per gram than carbohydrates or proteins.
Lipids serve as physical and thermal insulation for the body, are key components in
cell membranes, and act as raw materials for the synthesis of hormones.
Lipids are mostly made up of hydrogen, carbon, and oxygen, Generally, they do not
dissolve in water, but dissolve in non-polar substances.
Some lipids form chains, while the others form rings.
There are four families of lipids:
1. Fats
2. Phospholipids
3. Steroids
4. Waxes
Lipids: fats
Fats are the most common form of energy storage and insulation in plants
and animals. They consist of one glycerol molecule and a maximum of
three fatty-acid chains. Each fatty-acid chain has a terminal carboxylic
acid, and contains between 16 and 18 carbons
A dehydration synthesis reaction creates the ester linkages that attach
the fatty acids to the glycerol. This process is called esterification. If the
fat is made up of three fatty-acid chains, it is called a triglyceride.
Fatty acids may be either saturated or unsaturated. Saturated fatty acids
have no double bonds between their carbon atoms and are saturated with
hydrogen atoms. These acids are solids at room temperature. Examples
include lard and butter. Unsaturated fatty acids have one or many double
bonds between carbons, so they are not saturated with hydrogen. They
are liquids at room temperature. Examples include corn oil and olive oil.
Lipids: Phospholipids
Phospholipids make up the cell membranes of an animal
cell.
They consist of a hydrophilic head and a hydrophobic
two-stranded tail.
They are composed of one glycerol, two fatty acids, and
a highly polar phosphate group.
The phospholipid bilayer in cells is virtually
impermeable to macromolecules, relatively
impermeable to charged ions, and quite permeable to
small, lipid-soluble molecules
Lipids: Steroids
Sterols are compact hydrophobic molecules containing four
fused hydrocarbon rings. Sterols are a subgroup of steroids.
Types of sterols include cholesterol and many other important
hormones.
Cholesterol is an important component of cell membranes
because it affects the membranes fluidity and acts as a
messenger in cell communication during development.
It can also be converted into vitamin D.
Other steroid compounds, such as sex hormones, control the
development of sex traits and gametes (egg and sperm cells)
Lipids: Waxes
Waxes are hydrophobic molecules that contain long-
chain fatty acids linked to alcohols or carbon rings.
Waxes often form waterproof coatings, such as
beeswax, paraffin, and the cuticle on plants leaves.
Waxes are used to manufacture items such as fuel,
candles, and furniture polish.
Proteins
Proteins are involved in almost everything cells do. They can be
enzymes, immunoglobulin, hemoglobin, keratin, fibrin, and so on.
Proteins are made up of many amino acids
Amino acids contain three distinct parts:
An amino group (NH2)
A carboxylic acid group (COOH)
A radical group (denoted by the letter R)
The 20 amino acids vary in the R groups they contain. These side chains
can make the amino acid polar (hydrophilic), non-polar (hydrophobic), or
charged (acidic/basic).
Eight of the amino acids are essential, meaning that we must obtain
these from our diet, while manufacturing the other 12 in our cells.
Proteins: Amino acids
Amino acids are the monomers that make up proteins.
The bonds that hold amino acids together are called
peptide bonds. Peptide bonds are formed by a
dehydration synthesis reaction.
Note that the carboxyl and amino functional groups are
involved in the formation of the peptide bond and
contribute atoms for the water molecule. The carboxyl
group from the serine gives up OH and the amino group
from glycine contributes H.
Protein Structure
Once proteins are formed, they fold up into compact
shapes. Although the shape of each protein is generally
globular (like rolled-up balls), these shapes are still very
specific, enabling them to carry out their specialized
functions within the cells.
The final shape of a protein is also called its
conformation.
The conformation is the result of the amino acid
sequence it contains and the interactions among those
amino acids
There are four stages of protein structure possible.
Protein structure
Primary structure: When proteins are first assembled, they
are said to be in their primary (1o ) structure.
This is a simple chain of amino acids joined together by
peptide bonds, or a polypeptide chain, as it is commonly
called.
The sequence of amino acids is determined by the nucleotide
(DNA) sequence of a particular gene.
With 20 different amino acids, there are endless possibilities
for the primary structure.
For instance, in a protein containing X number of amino acids,
the number of possibilities is 20x
Protein structure
Secondary structure: As the amino acid assembly process creates the primary structure, the
protein chain begins folding and coiling as it grows.
Secondary structures are formed by hydrogen bonds between the oxygen atoms of a carboxyl
group and the hydrogen atoms of an amino group. There are two types of secondary structures:
helix: A tight coil produced by hydrogen bonds occurring at every fourth peptide bond. This
bonding is repeated along the entire length of the polypeptide to form a twisted rope.
pleated sheets: Hydrogen bonds formed between parallel stretches of a polypeptide to form
sheets
Tertiary structure: The polypeptide chain undergoes additional folding, due to sidechain (R-
group) interactions.
The most common are covalent bonds between sulphur atoms, called disulphide bridges. These
bridges help to form the globular structure called the tertiary structure. All proteins eventually
settle into their tertiary structure.
Quaternary structure: In some cases, two or more polypeptides join together to make a
functional protein. In this case, the final structure depends on how the two or more polypeptides
fold together. This is called the quaternary structure. It occurs when two or more folded
polypeptide chains come together, such as those in collagen and hemoglobin.
Protein structure
Nucleic acid
Nucleic acids are found in DNA (deoxyribonucleic acid), RNA
(ribonucleic acid), ATP (adenosine triphosphate), and nucleotide
coenzymes (NAD+ , NADP+ , and FAD).
DNA and RNA are called nucleotide polymers. Nucleotides consist of
a nitrogenous base, a five-carbon sugar, and a phosphate group.
The phosphate and ribose groups are joined together by a
phosphodiester linkage.
The five nitrogenous bases: 1. Adenine (A), 2. Guanine (G), 3.
Cytosine (C), 4. Thymine (T), 5. Uracil (U)
Adenine and guanine are called purines. They have a double-ring
structure. Cytosine, thymine, and uracil are called pyrimidines and
have a single-ring structure.
Macromolecule testing
There are two tests that test for carbohydrates the
Benedicts reagent tests for simple sugars and the Iodine
test (using Lugols solution) for polysaccharides, such as
starch. Benedicts reagent is a light blue reagent which,
when added to a substance containing simple sugar,
changes colour. The iodine solution turns from light brown to
a deep purple-black, if starch is present.
Sudan IV lipid test- turns from a pink to a red colour, if
lipids are present.
Biurets protein test- Biurets reagent changes from light
blue to a deep purple if proteins are present.
Enzymes Lesson 3 (unit 3)
Enzymes are proteins; they are composed of amino acids arranged in tertiary or
quaternary structures, with complex (shapes).
Enzymes can be used to join together two molecules or break one molecule into two
parts.
The names of enzymes usually end in -ase. For example, there is a specific enzyme
called maltase, which is used to hydrolyze (or break down) maltose, and another called
sucrase, which is used to break down sucrose. In these cases, the enzymes involved
break the complex sugar molecules down into their monosaccharide monomers.
Enzymes are specific to a particular substrate (reactant). For instance, the enzyme
maltase cannot hydrolyze the substrate sucrose, and sucrase cannot hydrolyze
maltose.
In order for a reaction to occur, the reactions have to overcome the activation energy
(Ea ) barrier. The activation energy is the amount of energy that must be available in
order for a reaction to occur.
Enzymes work by lowering the activation energy.
Enzymes
Enzymes
Enzymes lower the activation energy required for the reaction to occur by attaching to the
reactants and positioning them so that they are in the optimal orientation to break or make
chemical bonds between them.
The reactants attach to special sites on the enzyme called active sites.
When reactants begin to interact with enzymes, they are called substrates. Each substrate
binds to the active site that is shaped exactly to fit that particular substrate, and no other.
The enzyme and its attached substrate form a structure called an enzyme-substrate complex.
Once the substrate begins to attach, the active site changes shape slightly to hold on to the
substrate and fine-tune its position. Its similar to what happens with your hand when you catch
a ball: your fingers automatically wrap around the ball to ensure that you dont drop it. This
change in shape (conformation) is called induced fit.
The active site continues to change shape until the substrate is completely bound. Once the
substrate is bound and optimally positioned by induced fit, the reaction can proceed to form or
break chemical bonds. The process of induced fit for splitting apart a molecule into two parts.
The process works in a similar way to combine two molecules into one.
Enzymes As shown in Figure 3.2, the enzyme and substrate
first combine on a specific area of the enzyme
called the active site, to form the enzyme
substrate complex. In this example, the enzyme is
sucrase and the substrate is sucrose. Then, the
enzyme substrate complex combines with water
(hydrolysis), which changes the shape of the
enzyme slightly so that the substrate can break
apart into glucose and fructose more easily. Next,
the reaction takes place and the sucrose molecule
is broken up into the two monomers, fructose and
glucose. Finally, the enzyme is released
unchanged, ready to react again with a new
substrate molecule
Enzymes
When splitting a molecule apart, enzymes decrease the energy of activation by
stretching and bending chemical bonds that need to break during the reaction.
Ex. This is similar to bending a thin twig so that it wont take much additional
energy to snap it.
When joining two molecules together, enzymes decrease the energy of activation
by forcing the molecules together in just the right way to cause bonds to form more
easily.
Ex. This is similar to what you do when you snap a button together: only when the
two parts are perfectly positioned can you easily snap them together.
Enzymes can also change the chemical environment around a molecule to
encourage a reaction. For example, it is thought that the acidic active site of the
enzyme may provide the low pH environment needed for certain reactions to take
place.
Enzymes may also need to work with other molecules as helpers. Some enzymes
require either non-protein cofactors, such as inorganic substances (Zn2+, Ca2+) or
organic coenzymes, before they can work properly. Coenzymes help by moving
molecules from one enzyme to another. Many coenzymes are derived from
vitamins. For example, the coenzyme NAD is a derivative of vitamin B3 (niacin).
Enzymes in the body
Enzymes play major roles in the digestive system, the respiratory system, and the
nervous system.
Digestion involves chemical reactions that break down food into basic building blocks of
glucose, fats, and amino acids the body needs. One critical enzyme in this process is
called pepsin. This enzyme is secreted into the stomach, where it breaks down proteins
into smaller pieces called peptides, so that they can be broken down further in the small
intestine. If this enzymes levels are too low, or its action is blocked (or inhibited), then
many proteins, like gluten (found in wheat and other grain products) and casein (found in
dairy products), are not completely digested, resulting in many health problems.
Respiration is the cellular process in which glucose is reacted with oxygen to produce
carbon dioxide and water, while releasing energy in controlled stages. One enzyme critical
in this process is called cytochrome c oxidase. This enzyme helps to combine the highly
reactive waste oxygen molecules produced during this process with hydrogen, to create
water. If this enzyme is absent, or its function is inhibited, then the process of cellular
respiration stops within seconds and death is rapid. Carbon monoxide is a potent inhibitor
of this enzyme.
Enzymes in the body contd
Your brain also relies on many enzymes to maintain optimal
conditions for neural processing.
For example, the enzyme acetylcholinesterase breaks down
acetylcholine, which is a neural transmitter.
Acetylcholine is a chemical that helps signals to pass between nerve
cells, but the system only works if the amount of acetylcholine is
strictly regulated.
If this enzyme is absent or inhibited, then excessive acetylcholine will
accumulate in the nerve synapses. This will cause paralysis in the
muscles, including those that control breathing, and lead to death.
The venom of many poisonous snakes includes chemicals that block
the activity of acetylcholinesterase.
Enzyme Activation and Inhibition
Although enzymes are important molecules involved in
chemical reactions, they need to be monitored, in terms
of when to be active (which is similar to having an on
and off light switch in a room).
For example, the enzyme lipase catalyzes the
breakdown of triglycerides into glycerol and fatty acids
When your body requires energy from triglycerides, it
will activate the lipase enzyme to break down fats.
When it does not require the lipid energy, it will inhibit
the lipase or turn it off.
Enzyme Inhibition
Enzymes can be inhibited or prevented from carrying out their
function, in a variety of ways.
Some of the inhibition occurs at the enzymes active site, which is
where the substrate binds when the enzyme is actively catalyzing
cell reactions.
Large enzymes with more than one subunit contain more than one
active site.
Most enzymes also contain an additional site, called the allosteric
site which is involved in turning the enzyme on and off.
If the enzyme inhibition happens on an active site, it is called
competitive inhibition. If it happens as a result of changes on the
allosteric site, it is called non-competitive inhibition.
Enzyme: Competitive Inhibitors
Competitive inhibitors are molecules that are so similar in shape to an enzymes substrate
that they can bind to the active site and block the normal substrate from binding.
Once the inhibitor has attached to the active site, the enzyme is unable to catalyze any
reactions at that site, the process happens quickly.
The competitive inhibitor molecule has a similar shape to that of the substrate. It binds to
the active site on the enzyme, preventing the normal substrate from binding to the site.
Many poisons act as competitive inhibitors on critical enzymes. For example, the poison
cyanide blocks the active site on cytochrome c oxidase and so stops cellular respiration
almost instantly.
Competitive inhibition does not necessarily result in the enzyme being fully turned off.
If an enzyme has more than one active site, then competitive inhibition can act to slow down
the rate of reaction of the enzyme by blocking some active sites, but leaving other active
sites open to hold substrates.
The more active sites there are that are blocked by inhibitors, the slower the overall rate of
reaction will be. In this way, the overall reaction rate can be controlled gradually. The
enzyme becomes completely inactive only if all of the active sites are blocked by inhibitors.
Enzyme: Non-competitive Inhibitors
Non-competitive inhibitors are molecules that bind to the enzyme at
another site on the enzyme, called the allosteric site (not the active
site). This changes the shape of the active site, thereby preventing
the normal substrate from successfully binding. This makes the
enzyme inactive.
This causes conformation (shape) change in the enzyme, preventing
the normal substrate from binding at any active site, this results in
the enzyme being turned off.
This process can also be used to activate an enzyme. Non-
competitive inhibition or non-competitive activation via the allosteric
site can provide a very sophisticated way to fine-tune the behaviour
of an enzyme. This method of enzyme control is called allosteric.
Enzyme: Allosteric Regulation
Enzymes can oscillate in shape between the on and off conformation
and can temporarily locked into the on or off shape by interacting with
other molecules called allosteric activators and inhibitors.
When these regulatory molecules bind to the allosteric or regulatory site
on the enzyme, they force a change in the shape of the enzyme.
Allosteric activators: These change the enzymes shape and stabilize it,
which keeps all of the active sites available for substrates to bind to (the
enzyme is on).
Allosteric inhibitors: These change the enzymes shape and stabilize it to
make all of the active sites unavailable to substrates (the enzyme is
off),
The enzyme stays in the on or off position until the allosteric regulator
is removed.
Feedback Inhibition
Feedback inhibition is a method that cells use to control metabolic
pathways, involving a series of sequential reactions in which each step is
catalyzed by a specific enzyme.
In this method of metabolic control, a product that is formed later in a
sequence of reactions allosterically inhibits an enzyme that catalyzes a
reaction occurring earlier in the process. It is a negative feedback process,
because as the amount of product produced increases, the rate of the
reaction decreases.
Ex. Enzyme 1 catalyzes the production of product A from two substrate
molecules. A metabolic pathway converts product A into product D, using
three other enzymes. Product D can act as an allosteric inhibitor on
enzyme 1. When the concentration of product D is high enough, it will
inhibit all of the available enzyme 1 molecules, and so stop the production
of product A. This effectively stops the metabolic process.
Factors that Affect Enzyme Activity
1. pH- Enzymes have optimal pH, depending on the environment of the substrate.
Some enzymes work best at a neutral pH (7), while others are active at acidic pH
ranges (34).
2. Temperature- Every enzyme has an optimal temperature at which it works best.
Most enzymes work best around 37C, the normal body temperature for mammals.
However, some organisms contain enzymes that function best at extremes of hot or
cold. In a later unit, you will learn about one of these enzymes, Taq polymerase, and
why it lies behind the biotechnology revolution.
3. The concentrations of the enzyme and substrate- Increasing the amount or
concentration of a substrate or enzyme will increase the number of successful
enzyme-substrate collisions, thereby increasing the enzyme activity. There is a
threshold point, however, beyond which there is no further increase in the enzymes
activity. This is the point of saturation. Saturation means that all of the enzyme
molecules are occupied with substrate. Adding more substrate will not increase the
rate of reaction because the enzymes are already working at full capacity.
Lesson 4(unit 1) The cell
Cell theory is based on three fundamental statements:
1. All living things are made up of cells.
This means that you, a bear, a flower, a giraffe, and every other living thing, are all made up of
cells.
2. The cell is the structural and functional unit of all living things.
All of your structures are made up of living cells, or, in some cases, the remains of dead cells. For
example, your heart is made up of cells, as are your skin and your hair.
3. All cells come from pre-existing cells by division.
Cells do not spontaneously come into being; they must come from other cells. You began as a
joining of two cellsa single sperm and an egg. This combination of cells made your first cell,
called a zygote. You have literally divided that first cell trillions of times to form the complex
multicellular human you now are.
Cell Organization - Cells are organized systems of chemicals working together. This hierarchy
starts with the atom, molecules or compounds, organelles, tissue, organ, organ system,
organism.
Cell Structure
All living things are composed of one or more cells.
The cell must be able to perform tasks, in order to stay
alive.
Cells have structures that enable them to ingest food,
excrete waste, and, in some cases, move around.
Specialized structures, known as organelles, work
together to make a cell function effectively.
Organelles in Animal Cells
Organelles: Small units that perform specialized functions within a cell.
Protoplasm: Protoplasm is the fluid substance in a cell that supports the organelles. The
protoplasm found in the nucleus is called nucleoplasm. The protoplasm found outside the
nucleus is called cytoplasm.
Cell membrane: The cell membrane separates the cells contents from its surrounding
environment. It controls the movement of materials in and out of the cell, and allows the
exchange of food and gases. The cell membrane (also called the plasma membrane) is one
of the most important organelles. Because of its importance, the structure and function of
cell membranes will be discussed in greater detail later on in this lesson.
Nucleus: The nucleus is the control centre of the cell. It contains the cells genetic material
(DNA) and is surrounded by a porous membrane called the nuclear membrane. The nucleus
is involved in cell division and is the storage area for all information and instructions for the
organelles.
Nucleolus: The nucleolus located within the nucleus manufactures ribosome parts.
Ribosomes: Ribosomes manufacture proteins in the cell. They are attached to the
endoplasmic reticulum or float freely in the cytoplasm.
Endoplasmic reticulum: The endoplasmic reticulum is a folded membrane that forms a
series of canals within the cytoplasm. It acts as a passageway for materials moving to and
from different parts of the cell and connects the nuclear membrane to the cell membrane.
When a portion of the endoplasmic reticulum (ER) is covered with ribosomes, it is called
rough endoplasmic reticulum (Rough ER). Portions that are free of ribosomes are called
smooth endoplasmic reticulum (Smooth ER).
Golgi bodies: Golgi bodies package protein and secrete it outside the cell.
Organelles in animal cells contd
Mitochondria: The mitochondrion (plural, mitochondria) is the powerhouse of the cell. It
produces energy, known as adenosine triphosphate (ATP), for cell functions.
Vacuoles: Vacuoles provide storage areas for food, minerals, and water.
Lysosomes: Lysosomes contain digestive enzymes that help to break down food molecules.
Waste molecules and other toxins are broken down by lysosomes and transported out of the cell
by vacuoles.
Microfilaments: Microfilaments are pipe-like structures that provide shape and support for cell
movement. They function as a cells skeleton.
Microtubules: Microtubules are protein-rich rods that provide pathways for organelle movement.
Centrioles: Centrioles are paired structures involved in animal cell division
Flagella: If present, a flagellum is used to help the cell move (swim) around.
Cilia: Cilia are like very fine hairs on the cells surface. They can be moved in coordinated waves
to enable the cell to travel around, or to sweep particles away. For example, the cells that line
your lungs have cilia that constantly move in order to remove debris, such as dust, that has
landed in the mucous of your respiratory tract.
The Cell Membrane
The cell membrane separates the cytoplasm from the external environment.
It acts like the cells security guard, controlling which chemicals can get in or out of the
cell.
The cell membrane allows essential molecules into the cell and allows metabolic waste to
leave. This means that the inside of a cell can be kept chemically different from its
external environment.
The cell membrane is composed mainly of phospholipids. A phospholipid consists of a
head, containing a phosphate group, and a long tail, made up of two fatty-acid chains.
The phosphate head region is hydrophilic (meaning water-loving) because it is water-
soluble. The reason why the head end is hydrophilic is because it contains a polar
phosphate (PO4) group. Recall that the water molecule is also polar because it has a
region of positive charge and a region of negative charge. Because polar molecules are
attracted to other polar molecules, the head end is attracted to water molecules.
The tail portions are hydrophobic (meaning water-fearing) and non-polar, because
they are not water-soluble. This means that the tail end wants to point away from water.
The hydrophobic tail contains one glycerol molecule attached to two fatty-acid chains,
which means that each part of the tail is attracted to fats or oils because it is made up of
fatty acids.
The Fluid-Mosaic of the Cell Membrane
The cell membrane is made up of a double layer of phospholipids called the
phospholipid bilayer. The outside layer is made up of the hydrophilic heads.
They face outward toward the watery environment.
The inside layer of the membrane is made up of the hydrophobic fatty-acid tails,
which face inward. Inserted into the membrane are proteins and cholesterol.
They can fit in because of the bends caused by the one unsaturated lipid layer. The
cholesterol molecules are free to drift around within the lipid bilayer to fix any
breaks in the membrane. Cholesterol also helps to maintain the fluid condition of
the bilayer. At low temperatures, cholesterol keeps the phospholipids apart, and at
higher temperatures, it attracts the phospholipids and stabilizes the membrane.
The proteins are called integral proteins, because they are embedded in the
membrane and function as channels through which ions and other molecules can
travel in and out of the cell. The combination of the lipid bilayer, the proteins, and
the cholesterol produces the fluid-mosaic model of the cell membrane.
It is called fluid because the membrane is not completely solid, giving it the
capability of allowing material to pass through it. It also means that the membrane
can constantly adjust itself to maintain a seal around the cytoplasm. It is called
mosaic because the membrane contains several kinds of molecules embedded in
it. One important type of protein embedded in the membrane is the glycoproteins,
which are proteins with an attached carbohydrate. They act as receptor sites for
hormones and aid in the cells adhesion to other cells.
Fluid mosaic model

Selective Permeability- The cell membrane


plays an essential role in regulating what enters
and leaves the cell. Because most living
membranes are able to control what passes
through them, they are described as being
selectively permeable.
Membrane Transport
The cell membrane provides a controlled gateway for
molecules moving in and out of the cell. There are three
processes by which molecules move in and out of the
cell:
1. Passive transport
2. Active transport
3. The use of vesicles to move very large molecules
around
Membrane transportation: Diffusion
Diffusion is the movement of molecules from an area of higher
concentration to an area of lower concentration.
Movement from an area of higher concentration to one of lower
concentration is known as moving along the concentration gradient.
When there is an equal concentration of particles in the solution it
is called equilibrium.
There are three factors that affect how fast diffusion occurs:
State of matter: Diffusion occurs more rapidly in a gas than in a
liquid. Temperature: Diffusion occurs more rapidly at higher
temperatures. Size of the molecule: Large molecules cannot
diffuse across cell membranes.
Membrane transportation: Diffusion:
osmosis
Osmosis is the diffusion of water across a selectively permeable membrane.
Water molecules move from a region of higher water (lower solute)
concentration to a region of lower water (higher solute) concentration.
This movement will continue until equilibrium is reached. You will conduct an
experiment on osmosis later on in the lesson.
Solutions are often categorized by their potential for osmosis across
membranes.
There are three categories:
Isotonic solution equal to the solute. Solute concentration is at equilibrium.
Hypertonic more solute than solution. Resulting in water diffusing out of the
cell by osmosis.
Hypotonic more solution(cytoplasm) than solute. Resulting in water diffusing
into the cell by osmosis
Membrane transportation: Facilitated Diffusion

Facilitated diffusion occurs when molecules enter cells with the aid of
helper molecules known as transport proteins.
Transport proteins move materials into or out of cells along the
concentration gradient (from high concentration to low concentration), no
energy is required.
The structure of these proteins enables them to be highly selective.
A particular transport protein will recognize and help move only one type
of dissolved molecule or ion, based on the particles shape, size, and
electrical charge.
In facilitated diffusion, larger molecules, such as glucose, move along the
concentration gradient from areas of higher concentration to areas of
lower concentration. This is helped by proteins embedded within the cell
membrane.
Membrane transportation: Active
Transport
The movement of materials across a cell membrane using the cells energy is
called active transport.
This is sometimes also called an active transport pump because the cell is
literally using energy to pump the molecules through the membrane,
against the concentration gradient. Sometimes a cell needs to create a large
concentration gradient for a certain molecule between the inside and outside
of the cell.
Since molecules, atoms, and ions naturally move with a concentration
gradient (from a higher to a lower concentration), this process requires the
cell to expend energy (in the form of ATP). This is why it is called active
transport.
Like facilitated diffusion, active transport relies on transport proteins to allow
substances to pass through the membrane. Active transport, however,
requires energy to move substances against the concentration gradient.
Membrane transportation: Active
transport
A cell uses active transport to maintain an intracellular environment that
is different from that outside the cell.
For example, it allows a cell to bring in and store nutrients that are
already in high concentration inside the cell. It also allows a cell to
completely remove harmful waste products from the intracellular
environment.
Active transport is necessary for homeostasisa process by which a
constant internal environment is maintained, despite changes in the
external environment.
The process of active transport requires an input of cellular energy
(ATP). (1) An ion is drawn onto the transport protein. (2) ATP is used to
move the ion through the membrane. (3) The ion is released inside, on
the other side of the membrane, where its concentration is higher
Membrane Transport Chart
Vesicles
Some molecules are too large to be transported through the cell membrane.
The cell uses a special method to move these molecules so that they do not
have to pass through the phospholipid bilayer.
The cell membrane can fold in on itself to wrap around and seal large
objects in a sac called a vesicle.
Like active transport, the cell must expend energy to use vesicles, in order
to transport larger molecules (such as proteins and polysaccharides) across
the cell membrane.
There are two ways in which vesicles are used to move materials across cell
membranes:
Endocytosis: to bring material in
Exocytosis: to take material out
Endocytosis
Endocytosis is the process by which cells ingest (take in)
large materials.
A portion of the cell (plasma) membrane surrounds the
material to be transported into the cell.
The pinched-in portion eventually breaks free from the
cell membrane and forms a vesicle in the cytoplasm. This
allows the material within the vesicle to travel to its final
destination within the cell.
There are three main types of endocytosis: phagocytosis,
pinocytosis, and receptor-mediated endocytosis.
Endocytosis
Vesicles: Endocytosis: phagocytosis,
pinocytosis
Phagocytosis (cell-eating): Phagocytosis is the
process where the cells engulf large, solid particles. For
example, this may occur when your immune cells (ie,
white blood cells) engulf invading bacteria to destroy
them. The trapped bacteria are digested after the
vesicle fuses with a lysosome inside the cell.
Pinocytosis (cell-drinking): Pinocytosis is the process
by which liquid droplets enter the cell, along with any
small particles they may contain. This occurs in nearly
all cell types, almost all of the time.
Vesicles: Endocytosis: Receptor-
mediated endocytosis
Receptor-mediated endocytosis (RME) enables the cell to acquire bulk quantities of
specific substances.
RME involves the use of receptors to recognize and bind molecules before they are
engulfed.
During RME, the molecule that is to enter the cell binds to special receptor proteins
located on the outside of the cell membrane.
Once enough molecules have gathered in an area, the cell membrane pinches in,
forming the vesicle that will transport these molecules into the cell. This process is
how molecules such as cholesterol enter the cell.
If a person consumes too much cholesterol in their diet, there wont be enough
receptors to handle it all.
Instead, the cholesterol builds up in the walls of the arteries and veins where it
hardens, forming a sticky substance called plaque.
This excess plaque can block blood vessels, leading to heart disease.
Exocytosis
Exocytosis uses vesicles to export large molecules out of
the cell.
This is useful for removing large waste particles.
For example, lysosomes often break down wastes and
other toxins inside the cell, and these wastes are then
transported out of the cell in a vesicle.
The vesicle is transported through the cytoplasm to fuse
with the cell membrane.
The cell membrane rearranges, opens, and releases the
contents of the vesicle outside the cell.
Cell Research in Medicine
Cancer cells reproduce in an abnormal manner. Cancer
patients often undergo treatments such as
chemotherapy to destroy the abnormal cancer cells.
One major problem with chemotherapy drugs is that
they are not able to target just the cancer cells; they kill
healthy cells as well.
Hybridomas are cells that have been engineered to
produce a desired antibody in large amounts.
Tissue cultures are groups of cells grown in a special
dish called a petri dish. These tissues can then be
implanted into an organism to assist in the organisms
growth and repair.