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.

Polar covalent bonds . • 3.Biochemistry: intramolecular bonds • There are three main types of intramolecular bonds: • 1. with one atom pulling harder on the electrons than the other.unequal sharing of valence electrons between atoms in the pair. .two or more non-metals share one or more pairs of electrons.one atom transfers electrons to another atom • 2. Ionic bonds . Covalent bonds .

.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 atom’s ability to attract electrons in a chemical bond.

• As a result. similar to that of a noble gas.Biochemistry: intramolecular: Covalent bond • A covalent bond forms when two or more non-metals share one or more pairs of electrons. • The simplest example of a covalent bond is between a diatomic molecule. the atoms end up with a stable electron arrangement in their outer orbit. .

• Whichever atom pulls the hardest on the electrons will become the slightly more negative pole (higher electronegativity). • This results in different ends of the molecule having different electric charges. while the other one will become more positive (lower electronegativity). slightly negative.Biochemistry: intramolecular: Polar Covalent bond • It is formed when there is an unequal sharing of valence electrons between atoms in the pair. • Because this results in two “poles. with one atom pulling harder on the electrons than the other. with one end being slightly positive and the other.” the molecule is said to be a dipole. .

Biochemistry: intermolecular forces • London forces . . Momentary dipoles are created by the electrons contained within the compound.Hold non-polar molecules together.Is formed between the electropositive hydrogen dipole and an electronegative dipole of oxygen. • Hydrogen bonding . or fluorine. • Dipole-dipole Forces . Very weak forces of attraction. which are constantly in motion. These forces are stronger than London forces.Hold polar molecules Together. chlorine.

Condensation 3. Hydrolysis 2.Biochemical reactions • There are four main reaction types that are important in biochemistry: 1. Neutralization reactions . Oxidation-reduction (redox) 4.

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 .

‘ • In most biochemical condensation reactions. • They are the opposite of hydrolysis reactions. • This is also known as dehydration synthesis because water is removed (“dehydrated”) in the synthesis of the new molecule.Biochemical reactions: Condensation • Condensation reactions occur when two molecules combine to form one molecule. • Amino acid + amino acid → protein + water (product is a synthsis and water) . water is produced when two smaller molecules join to produce a larger molecule.

Biochemical reactions: redox Reduction and oxidation LEO says GER – lose electron oxidation. The zinc atoms in solid form lose two electrons to form zinc ions in aqueous form (Zn(s) → Zn+2(aq)). . (produce ATP in body) • Zn(s) + Cu2+(aq) → Cu(s) + Zn2+(aq) • Notice what happens to the reactants in this equation. Meanwhile. and so is commonly called a redox reaction. • An electron transfer between two substances always involves a reduction of one and an oxidation of the other. the copper ions in aqueous form gain two electrons to form copper atoms in solid form (Cu2+(aq) → Cu(s)). • The process of gaining electrons is called reduction. gain electron reduction • The process of losing electrons is called oxidation.

sodium hydroxide (NaOH) and hydrochloric acid (HCl) react together to form the salt. 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. sodium chloride (NaCl). thus neutralizing excess acid or base. • When an acid reacts with a base.this happens by taking up excess hydrogen or hydroxide ions. a neutralization reaction occurs because water is produced from the H+ and OH– ions in solution. • One way in which organisms use the neutralization reaction to regulate internal pH using a system of acid-base buffers. For example.Biochemical reactions: Neutralization • Neutralization reactions are the reaction of an acid and a base to produce water and a salt. which determines the speed and direction of many critical biological reactions such as DNA synthesis. .

•It has a pH of below 7. •It has a pH of above 7. •It conducts electricity. •The hydrogen ion have pH values of below 7. when dissolved in water. H2O → OH– + H+ The ions in the water create the properties of an acid and a base. ( increase H+ in water) have the following characteristics of an acidic solution: •It has a sour taste. as well as a tiny number of H+ and OH– ions. increase the concentration of the hydrogen ions. increase the concentration of hydroxide ions. Bases are substances that. •It turns litmus paper red. Biochemical reactions: Neutralization •Properties of Acids and Bases Pure water contains H2O molecules. 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. through a natural process of ionization. . •Acids are substances that. when dissolved in water. •It turns litmus paper blue. •The hydroxide ion.

sodium hydroxide. 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 .Biochemical reactions: Neutralization: acids and bases •• Acids and bases may be classified as strong or weak. such as vinegar. acetic acid. Strong acids (for example. NaOH) ionize completely when • dissolved in water: • HCl(aq) + H2O → H3 + Cl– • NaOH(aq) → + OH– • Weak acids (for example. CH3COOH) and weak bases (for • example. hydrochloric acid. HCl) • and strong bases (for example. ammonia. depending on the degree to   which they ionize when dissolved in water.

Lesson 2.Structure and Function of biomolecules (functional groups) .

Nucleic acids . Carbohydrates • 2.Structure and Function of biomolecules • The functional groups are hydrophilic. process called hydrolysis) • The four macromolecules of life: • 1. H2O removed from reaction) • catabolic (breaking down to monomer using water. • Macromolecules are large molecules made up of smaller repeating units called Monomers.Lesson 2. • anabolic (building-up to macromolecules using condensation. Lipids • 3. Proteins • 4.

Polysaccharides . Monosaccharides. and for cell identification and communication. They all have the same molecular formula: C6H12O6 2.Structure and Function of biomolecules: Carbohydrates • Carbohydrates used as building materials for energy. • Carbohydrates are classified into three groups: 1.Lesson 2. and fructose. Oligosaccharides - 3.The most important monosaccharides are isomers of each other: glucose. galactose. .

• When dissolved in water. • These sugars are distinguished from one another by the carbonyl group they possess.All carbons have hydroxyl groups attached. When dry. • There are two types of monosaccharide: • Aldoses.All carbons have hydroxyl groups attached. are called isomers. with the exception of a carbonyl group found the second carbon.” and “saccharide” means “sugar”) are simple chains that can form rings when they dissolve in water. sugars with five or more carbons form ring structures. . Fructose. with the exception of a carbonyl group found on the last carbon. Glucose.Monosaccharides • Monosaccharides (“mono-” means “one. galactose • Ketoses. they form linear structures. but in a different “order” or arrangement. ribulose • Molecules that contain the same atoms. ribose.

• Glucose + glucose → maltose + water • Glucose + fructose → sucrose + water • Glucose + galactose → lactose + water . maltose. • Glycosidic linkages are formed from dehydration synthesis reactions. and sucrose. attached to one another by covalent bonds.Oligosaccharides • Oligosaccharides (“oligo-” means “few”) contain two or three simple sugars. • These reactions form disaccharides such as lactose. called glycosidic linkages.

Glycogen 3. • There are four types of polysaccharides: 1.Polysaccharides • Polysaccharides are polymers composed of several hundred to several thousand monosaccharide subunits. Chitin. held together by glycosidic linkages. Starch 2. Cellulose 4. • These molecules are very important in our diet and provide much of nature’s building material. .

Root vegetables. Enzymes in the liver and muscles can also break glycogen molecules apart. such as carrots and potatoes. but glycogen is more branched than starch. have an abundance of starch. when glucose is required. • As glucose increases. which humans can digest for energy. • For example. • It is the primary energy storage molecule for plants. . • Glycogen regulates blood glucose levels. and α1-6 links where it branches. glycogen • Starch is composed of amylose (with α1-4 links) and amylopectin (with α1-6 links).Polysaccharides: starch. adrenalin stimulates the breakdown of chemical bonds in a glycogen chain for quick energy. • Like starch. glycogen is composed of α1-4 links. such as that needed for an animal’s “flight or fight” reaction when it is confronted with danger. It is the main energy storage molecule for animals. the liver and muscles convert excess glucose to glycogen.

Polysaccharides: Cellulose, Chitin
• Cellulose is composed of β1-4 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. relatively impermeable to charged ions. and quite permeable to small. lipid-soluble molecules . two fatty acids. • They are composed of one glycerol. and a highly polar phosphate group. • The phospholipid bilayer in cells is virtually impermeable to macromolecules.

control the development of sex traits and gametes (egg and sperm cells) . Sterols are a subgroup of steroids. • Types of sterols include cholesterol and many other important hormones. such as sex hormones. • It can also be converted into vitamin D. • Cholesterol is an important component of cell membranes because it affects the membrane’s fluidity and acts as a messenger in cell communication during development.Lipids: Steroids • Sterols are compact hydrophobic molecules containing four fused hydrocarbon rings. • Other steroid compounds.

and the cuticle on plants’ leaves. • Waxes are used to manufacture items such as fuel. • Waxes often form waterproof coatings. and furniture polish.Lipids: Waxes • Waxes are hydrophobic molecules that contain long- chain fatty acids linked to alcohols or carbon rings. such as beeswax. paraffin. . candles.

meaning that we must obtain these from our diet. • Eight of the amino acids are essential. • 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. . They can be enzymes. keratin. while manufacturing the other 12 in our cells. non-polar (hydrophobic). or charged (acidic/basic). These side chains can make the amino acid polar (hydrophilic).Proteins • Proteins are involved in almost everything cells do. fibrin. hemoglobin. and so on. immunoglobulin.

Peptide bonds are formed by a dehydration synthesis reaction. . The carboxyl group from the serine gives up OH and the amino group from glycine contributes H. The bonds that hold amino acids together are called peptide bonds.Proteins: Amino acids • Amino acids are the monomers that make up proteins. • 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 final shape of a protein is also called its conformation. these shapes are still very specific.Protein Structure • Once proteins are formed. enabling them to carry out their specialized functions within the cells. they fold up into compact shapes. Although the shape of each protein is generally globular (like rolled-up balls). • 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.

the number of possibilities is 20x .” as it is commonly called. there are endless possibilities for the primary structure. in a protein containing X number of amino acids. or a “polypeptide chain. • The sequence of amino acids is determined by the nucleotide (DNA) sequence of a particular gene. • For instance. • With 20 different amino acids. they are said to be in their primary (1o ) structure. • This is a simple chain of amino acids joined together by peptide bonds.Protein structure • Primary structure: When proteins are first assembled.

called disulphide bridges. . This bonding is repeated along the entire length of the polypeptide to form a twisted “rope. the final structure depends on how the two or more polypeptides fold together. In this case. two or more polypeptides join together to make a functional protein. the protein chain begins folding and coiling as it grows. • The most common are covalent bonds between sulphur atoms. It occurs when two or more folded polypeptide chains come together.” • β pleated sheets: Hydrogen bonds formed between parallel stretches of a polypeptide to form sheets • Tertiary structure: The polypeptide chain undergoes additional folding. There are two types of secondary structures: • α helix: A tight coil produced by hydrogen bonds occurring at every fourth peptide bond.Protein structure • Secondary structure: As the amino acid assembly process creates the primary structure. due to sidechain (“R”- group) interactions. such as those in collagen and hemoglobin. This is called the quaternary structure. These bridges help to form the globular structure called the tertiary structure. • Quaternary structure: In some cases. All proteins eventually settle into their tertiary structure. • Secondary structures are formed by hydrogen bonds between the oxygen atoms of a carboxyl group and the hydrogen atoms of an amino group.

Protein structure .

5. 2. NADP+ . RNA (ribonucleic acid). Guanine (G). and FAD). . a five-carbon sugar. ATP (adenosine triphosphate). 4. Cytosine (C). 3. Adenine (A). • The phosphate and ribose groups are joined together by a phosphodiester linkage. • DNA and RNA are called nucleotide polymers. and a phosphate group. They have a double-ring structure. and nucleotide coenzymes (NAD+ .Nucleic acid • Nucleic acids are found in DNA (deoxyribonucleic acid). thymine. Uracil (U) • Adenine and guanine are called purines. Thymine (T). • The five nitrogenous bases: 1. Nucleotides consist of a nitrogenous base. and uracil are called pyrimidines and have a single-ring structure. Cytosine.

if lipids are present. Benedict’s reagent is a light blue reagent which. .Biuret’s reagent changes from light blue to a deep purple if proteins are present. • Sudan IV lipid test.turns from a pink to a red colour. when added to a substance containing simple sugar. • Biuret’s protein test.Macromolecule testing • There are two tests that test for carbohydrates the Benedict’s reagent tests for simple sugars and the Iodine test (using Lugol’s solution) for polysaccharides. changes colour. such as starch. if starch is present. The iodine solution turns from light brown to a deep purple-black.

• The names of enzymes usually end in “-ase. there is a specific enzyme called maltase. • Enzymes can be used to join together two molecules or break one molecule into two parts. For instance. and sucrase cannot hydrolyze maltose. the reactions have to overcome the activation energy (Ea ) barrier. • Enzymes work by lowering the activation energy. . the enzymes involved break the complex sugar molecules down into their monosaccharide monomers.Enzymes Lesson 3 (unit 3) • Enzymes are proteins. which is used to break down sucrose. • Enzymes are specific to a particular substrate (reactant). they are composed of amino acids arranged in tertiary or quaternary structures.” For example. • In order for a reaction to occur. In these cases. The activation energy is the amount of energy that must be available in order for a reaction to occur. with complex (shapes). which is used to hydrolyze (or break down) maltose. and another called sucrase. the enzyme maltase cannot hydrolyze the substrate sucrose.

Enzymes .

the reaction can proceed to form or break chemical bonds.” • When reactants begin to interact with 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. .” • Once the substrate begins to attach.” • The active site continues to change shape until the substrate is completely bound. This change in shape (conformation) is called “induced fit. and no other. • The enzyme and its attached substrate form a structure called an “enzyme-substrate complex. Each substrate binds to the active site that is shaped exactly to fit that particular substrate. Once the substrate is bound and optimally positioned by induced fit. they are called substrates. • The process works in a similar way to combine two molecules into one. The process of induced fit for splitting apart a molecule into two parts. the active site changes shape slightly to hold on to the substrate and fine-tune its position. It’s similar to what happens with your hand when you catch a ball: your fingers automatically wrap around the ball to ensure that you don’t drop it.

the enzyme is released unchanged. which changes the shape of the enzyme slightly so that the substrate can break apart into glucose and fructose more easily. Next.Enzymes As shown in Figure 3.2. to form the enzyme substrate complex. Then. the enzyme is sucrase and the substrate is sucrose. Finally. ready to react again with a new substrate molecule . the reaction takes place and the sucrose molecule is broken up into the two monomers. In this example. the enzyme and substrate first combine on a specific area of the enzyme called the active site. the enzyme substrate complex combines with water (hydrolysis). fructose and glucose.

• When joining two molecules together. 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. Coenzymes help by moving molecules from one enzyme to another. • Ex.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. For example. before they can work properly. such as inorganic substances (Zn2+. the coenzyme NAD– is a derivative of vitamin B3 (niacin). . • Ex. enzymes decrease the energy of activation by forcing the molecules together in just the right way to cause bonds to form more easily. • Enzymes may also need to work with other molecules as helpers. Many coenzymes are derived from vitamins. Ca2+) or organic coenzymes. This is similar to bending a thin twig so that it won’t take much additional energy to snap it. 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. Some enzymes require either non-protein cofactors. • Enzymes can also change the chemical environment around a molecule to encourage a reaction.

or its action is blocked (or “inhibited”).Enzymes in the body • Enzymes play major roles in the digestive system. • Respiration is the cellular process in which glucose is reacted with oxygen to produce carbon dioxide and water. while releasing energy in controlled stages. and amino acids the body needs. This enzyme is secreted into the stomach. then the process of cellular respiration stops within seconds and death is rapid. or its function is inhibited. One enzyme critical in this process is called cytochrome c oxidase. like gluten (found in wheat and other grain products) and casein (found in dairy products). • Digestion involves chemical reactions that break down food into basic building blocks of glucose. are not completely digested. then many proteins. and the nervous system. resulting in many health problems. If this enzyme’s levels are too low. where it breaks down proteins into smaller pieces called peptides. fats. This enzyme helps to combine the highly reactive waste oxygen molecules produced during this process with hydrogen. Carbon monoxide is a potent inhibitor of this enzyme. . the respiratory system. One critical enzyme in this process is called pepsin. to create water. so that they can be broken down further in the small intestine. If this enzyme is absent.

and lead to death. • If this enzyme is absent or inhibited. • The venom of many poisonous snakes includes chemicals that block the activity of acetylcholinesterase. then excessive acetylcholine will accumulate in the nerve synapses.Enzymes in the body cont’d • Your brain also relies on many enzymes to maintain optimal conditions for neural processing. the enzyme acetylcholinesterase breaks down acetylcholine. including those that control breathing. but the system only works if the amount of acetylcholine is strictly regulated. • For example. This will cause paralysis in the muscles. . which is a neural transmitter. • Acetylcholine is a chemical that helps signals to pass between nerve cells.

it will “activate” the lipase enzyme to break down fats.Enzyme Activation and Inhibition • Although enzymes are important molecules involved in chemical reactions. they need to be monitored.” . • When it does not require the lipid energy. • For example. it will inhibit the lipase or “turn it off. the enzyme lipase catalyzes the breakdown of triglycerides into glycerol and fatty acids • When your body requires energy from triglycerides. in terms of when to be active (which is similar to having an “on” and “off” light switch in a room).

in a variety of ways. • Some of the inhibition occurs at the enzyme’s active site. If it happens as a result of changes on the allosteric site. . • Most enzymes also contain an additional site. • Large enzymes with more than one subunit contain more than one active site. called the allosteric site which is involved in turning the enzyme “on” and “off. it is called non-competitive inhibition.Enzyme Inhibition • Enzymes can be inhibited or prevented from carrying out their function. which is where the substrate binds when the enzyme is actively catalyzing cell reactions. it is called competitive inhibition.” • If the enzyme inhibition happens on an active site.

the process happens quickly. • Once the inhibitor has attached to the active site. but leaving other active sites open to hold substrates. • The competitive inhibitor molecule has a similar shape to that of the substrate. then competitive inhibition can act to slow down the rate of reaction of the enzyme by blocking some active sites. . • The more active sites there are that are blocked by inhibitors.Enzyme: Competitive Inhibitors • Competitive inhibitors are molecules that are so similar in shape to an enzyme’s substrate that they can bind to the active site and block the normal substrate from binding. preventing the normal substrate from binding to the site. It binds to the active site on the enzyme.” • If an enzyme has more than one active site. the enzyme is unable to catalyze any reactions at that site. • Many poisons act as competitive inhibitors on critical enzymes. The enzyme becomes completely inactive only if all of the active sites are blocked by inhibitors. the poison cyanide blocks the active site on cytochrome c oxidase and so stops cellular respiration almost instantly. the slower the overall rate of reaction will be. In this way. • Competitive inhibition does not necessarily result in the enzyme being fully “turned off. For example. the overall reaction rate can be controlled gradually.

• This process can also be used to activate an enzyme. This changes the shape of the active site. called the allosteric site (not the active site).Enzyme: Non-competitive Inhibitors • Non-competitive inhibitors are molecules that bind to the enzyme at another site on the enzyme. this results in the enzyme being turned off. • This causes conformation (shape) change in the enzyme. thereby preventing the normal substrate from successfully binding. . This method of enzyme control is called allosteric. preventing the normal substrate from binding at any active site. This makes the enzyme inactive. 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.

• Allosteric activators: These change the enzyme’s shape and stabilize it. • When these regulatory molecules bind to the allosteric or regulatory site on the enzyme. which keeps all of the active sites available for substrates to bind to (the enzyme is “on”). • Allosteric inhibitors: These change the enzyme’s shape and stabilize it to make all of the active sites unavailable to substrates (the enzyme is “off”).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. they force a change in the shape of the enzyme. . • The enzyme stays in the “on” or “off” position until the allosteric regulator is removed.

This effectively stops the metabolic process. and so stop the production of product A.Feedback Inhibition • Feedback inhibition is a method that cells use to control metabolic pathways. . the rate of the reaction decreases. • Ex. Product D can act as an allosteric inhibitor on enzyme 1. using three other enzymes. a product that is formed later in a sequence of reactions allosterically inhibits an enzyme that catalyzes a reaction occurring earlier in the process. involving a series of sequential reactions in which each step is catalyzed by a specific enzyme. it will inhibit all of the available enzyme 1 molecules. When the concentration of product D is high enough. Enzyme 1 catalyzes the production of product A from two substrate molecules. A metabolic pathway converts product A into product D. It is a negative feedback process. because as the amount of product produced increases. • In this method of metabolic control.

The concentrations of the enzyme and substrate. In a later unit. some organisms contain enzymes that function best at extremes of hot or cold. However. Taq polymerase. Saturation means that all of the enzyme molecules are occupied with substrate.Every enzyme has an optimal temperature at which it works best. depending on the environment of the substrate. Adding more substrate will not increase the rate of reaction because the enzymes are already working at full capacity. however. pH.Increasing the amount or concentration of a substrate or enzyme will increase the number of successful enzyme-substrate collisions. and why it lies behind the biotechnology revolution. Temperature. while others are active at acidic pH ranges (3–4). This is the point of saturation. 2.Enzymes have optimal pH. Some enzymes work best at a neutral pH (7). thereby increasing the enzyme activity. beyond which there is no further increase in the enzyme’s activity. you will learn about one of these enzymes. . the normal body temperature for mammals. Most enzymes work best around 37C. 3. There is a threshold point.Factors that Affect Enzyme Activity 1.

All cells come from pre-existing cells by division. or. tissue. This combination of cells made your first cell. organism. Cell Organization . You have literally divided that first cell trillions of times to form the complex multicellular human you now are. . organ. molecules or compounds. they must come from other cells. as are your skin and your hair. All living things are made up of cells. your heart is made up of cells. This means that you. • 3.Lesson 4(unit 1) The cell Cell theory is based on three fundamental statements: • 1. a flower. For example. a giraffe. organelles. are all made up of cells. a bear.Cells are organized systems of chemicals working together. All of your structures are made up of living cells. in some cases. called a zygote. the remains of dead cells. This hierarchy starts with the atom. organ system. and every other living thing. • 2. Cells do not spontaneously come into being. You began as a joining of two cells—a single sperm and an egg. The cell is the structural and functional unit of all living things.

in some cases. in order to stay alive. • Specialized structures. excrete waste. .Cell Structure • All living things are composed of one or more cells. and. • The cell must be able to perform tasks. known as organelles. • Cells have structures that enable them to ingest food. work together to make a cell function effectively. move around.

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• Nucleolus: The nucleolus located within the nucleus manufactures ribosome parts. 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. It controls the movement of materials in and out of the cell. The protoplasm found in the nucleus is called nucleoplasm. They are attached to the endoplasmic reticulum or float freely in the cytoplasm. Portions that are free of ribosomes are called smooth endoplasmic reticulum (Smooth ER). • Protoplasm: Protoplasm is the fluid substance in a cell that supports the organelles. When a portion of the endoplasmic reticulum (ER) is covered with ribosomes. • Nucleus: The nucleus is the control centre of the cell. it is called rough endoplasmic reticulum (Rough ER). Organelles in Animal Cells • Organelles: Small units that perform specialized functions within a cell. • Cell membrane: The cell membrane separates the cell’s contents from its surrounding environment. It contains the cell’s genetic material (DNA) and is surrounded by a porous membrane called the nuclear membrane. . Because of its importance. The cell membrane (also called the plasma membrane) is one of the most important organelles. and allows the exchange of food and gases. The protoplasm found outside the nucleus is called cytoplasm. The nucleus is involved in cell division and is the storage area for all information and instructions for the organelles. • Ribosomes: Ribosomes manufacture proteins in the cell. • Endoplasmic reticulum: The endoplasmic reticulum is a folded membrane that forms a series of canals within the cytoplasm. the structure and function of cell membranes will be discussed in greater detail later on in this lesson. • Golgi bodies: Golgi bodies package protein and secrete it outside the cell.

Organelles in animal cells cont’d • Mitochondria: The mitochondrion (plural. the cells that line your lungs have cilia that constantly move in order to remove debris. mitochondria) is the powerhouse of the cell. known as adenosine triphosphate (ATP). such as dust. or to sweep particles away. For example. a flagellum is used to help the cell move (swim) around. for cell functions. They function as a cell’s skeleton. • Lysosomes: Lysosomes contain digestive enzymes that help to break down food molecules. They can be moved in coordinated waves to enable the cell to travel around. • Microtubules: Microtubules are protein-rich rods that provide pathways for organelle movement. minerals. • Centrioles: Centrioles are paired structures involved in animal cell division • Flagella: If present. • Microfilaments: Microfilaments are pipe-like structures that provide shape and support for cell movement. Waste molecules and other toxins are broken down by lysosomes and transported out of the cell by vacuoles. • Cilia: Cilia are like very fine hairs on the cell’s surface. • Vacuoles: Vacuoles provide storage areas for food. It produces energy. that has landed in the mucous of your respiratory tract. and water. .

” made up of two fatty-acid chains. The phosphate “head” region is hydrophilic (meaning “water-loving”) because it is water- soluble. because they are not water-soluble.The Cell Membrane • The cell membrane separates the cytoplasm from the external environment. Recall that the water molecule is also polar because it has a region of positive charge and a region of negative charge. The reason why the head end is hydrophilic is because it contains a polar phosphate (PO4) group. A phospholipid consists of a “head.” containing a phosphate group. This means that the inside of a cell can be kept chemically different from its external environment. Because polar molecules are attracted to other polar molecules. the head end is attracted to water molecules. . • It acts like the cell’s “security guard. and a long “tail. The hydrophobic tail contains one glycerol molecule attached to two fatty-acid chains. • The cell membrane is composed mainly of phospholipids. which means that each part of the tail is attracted to fats or oils because it is made up of fatty acids.” controlling which chemicals can get in or out of the cell. • The “tail” portions are hydrophobic (meaning “water-fearing”) and non-polar. This means that the tail end wants to point away from water. • The cell membrane allows essential molecules into the cell and allows metabolic waste to leave.

• The proteins are called integral proteins. The combination of the lipid bilayer. It is called “mosaic” because the membrane contains several kinds of molecules embedded in it. They face outward toward the watery environment. it attracts the phospholipids and stabilizes the membrane. They can fit in because of the bends caused by the one unsaturated lipid layer. • It is called “fluid” because the membrane is not completely solid. giving it the capability of allowing material to pass through it. One important type of protein embedded in the membrane is the glycoproteins. At low temperatures. • The inside layer of the membrane is made up of the hydrophobic fatty-acid tails. The cholesterol molecules are free to drift around within the lipid bilayer to fix any breaks in the membrane. It also means that the membrane can constantly adjust itself to maintain a seal around the cytoplasm. Inserted into the membrane are proteins and cholesterol. cholesterol keeps the phospholipids apart. The outside layer is made up of the hydrophilic heads. and the cholesterol produces the fluid-mosaic model of the cell membrane. and at higher temperatures. Cholesterol also helps to maintain the fluid condition of the bilayer. They act as receptor sites for hormones and aid in the cell’s adhesion to other cells. which are proteins with an attached carbohydrate. 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. which face inward. the proteins. .The Fluid-Mosaic of the Cell Membrane • The cell membrane is made up of a double layer of phospholipids called the phospholipid bilayer.

Because most living membranes are able to control what passes through them.The cell membrane plays an essential role in regulating what enters and leaves the cell. they are described as being selectively permeable. .Fluid mosaic model Selective Permeability.

The use of vesicles to move very large molecules around . There are three processes by which molecules move in and out of the cell: 1. Passive transport 2. Active transport 3.Membrane Transport • The cell membrane provides a controlled gateway for molecules moving in and out of the cell.

• When there is an equal concentration of particles in the solution it is called equilibrium. . Size of the molecule: Large molecules cannot diffuse across cell membranes.Membrane transportation: Diffusion • Diffusion is the movement of molecules from an area of higher concentration to an area of lower concentration. • 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. • Movement from an area of higher concentration to one of lower concentration is known as moving along the concentration gradient.

Resulting in water diffusing out of the cell by osmosis. You will conduct an experiment on osmosis later on in the lesson. • Hypertonic – more solute than solution. • This movement will continue until equilibrium is reached. • There are three categories: • Isotonic – solution equal to the solute. Water molecules move from a region of higher water (lower solute) concentration to a region of lower water (higher solute) concentration. Solute concentration is at equilibrium. • Solutions are often categorized by their potential for osmosis across membranes.Membrane transportation: Diffusion: osmosis • Osmosis is the diffusion of water across a selectively permeable membrane. Resulting in water diffusing into the cell by osmosis . • Hypotonic – more solution(cytoplasm) than solute.

and electrical charge. This is helped by proteins embedded within the cell membrane. move along the concentration gradient from areas of higher concentration to areas of lower concentration. larger molecules. no energy is required.Membrane transportation: Facilitated Diffusion • Facilitated diffusion occurs when molecules enter cells with the aid of “helper molecules” known as transport proteins. . • A particular transport protein will recognize and help move only one type of dissolved molecule or ion. based on the particle’s shape. • Transport proteins move materials into or out of cells along the concentration gradient (from high concentration to low concentration). • In facilitated diffusion. • The structure of these proteins enables them to be highly selective. such as glucose. size.

Active transport. atoms. against the concentration gradient. . however. • Since molecules. • This is sometimes also called an active transport pump because the cell is literally using energy to “pump” the molecules through the membrane. requires energy to move substances 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. Membrane transportation: Active Transport • The movement of materials across a cell membrane using the cell’s energy is called active transport. and ions naturally move with a concentration gradient (from a higher to a lower concentration). This is why it is called active transport. active transport relies on transport proteins to allow substances to pass through the membrane. this process requires the cell to expend energy (in the form of ATP). • Like facilitated diffusion.

(1) An ion is drawn onto the transport protein. despite changes in the external environment. it allows a cell to bring in and store nutrients that are already in high concentration inside the cell. (3) The ion is released inside. • For example.Membrane transportation: Active transport • A cell uses active transport to maintain an intracellular environment that is different from that outside the cell. • The process of active transport requires an input of cellular energy (ATP). (2) ATP is used to move the ion through the membrane. where its concentration is higher . It also allows a cell to completely remove harmful waste products from the intracellular environment. on the other side of the membrane. • Active transport is necessary for homeostasis—a process by which a constant internal environment is maintained.

Membrane Transport Chart .

the cell must expend energy to use vesicles.Vesicles • Some molecules are too large to be transported through 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 . in order to transport larger molecules (such as proteins and polysaccharides) across 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. • Like active transport. • The cell membrane can fold in on itself to wrap around and seal large objects in a sac called a vesicle.

pinocytosis. This allows the material within the vesicle to travel to its final destination within the cell. • The “pinched-in” portion eventually breaks free from the cell membrane and forms a vesicle in the cytoplasm.Endocytosis • Endocytosis is the process by which cells ingest (take in) large materials. . and receptor-mediated endocytosis. • A portion of the cell (plasma) membrane surrounds the material to be transported into the cell. • There are three main types of endocytosis: phagocytosis.

Endocytosis .

along with any small particles they may contain. This occurs in nearly all cell types. white blood cells) engulf invading bacteria to destroy them. For example. solid particles. almost all of the time. The trapped bacteria are digested after the vesicle fuses with a lysosome inside the cell.Vesicles: Endocytosis: phagocytosis. this may occur when your immune cells (ie. . • Pinocytosis (“cell-drinking”): Pinocytosis is the process by which liquid droplets enter the cell. pinocytosis • Phagocytosis (“cell-eating”): Phagocytosis is the process where the cells engulf large.

Vesicles: Endocytosis: Receptor- mediated endocytosis • Receptor-mediated endocytosis (RME) enables the cell to acquire bulk quantities of specific substances. • If a person consumes too much cholesterol in their diet. forming the vesicle that will transport these molecules into the cell. the cholesterol builds up in the walls of the arteries and veins where it hardens. leading to heart disease. This process is how molecules such as cholesterol enter the cell. forming a sticky substance called plaque. • This excess plaque can block blood vessels. • RME involves the use of receptors to recognize and bind molecules before they are engulfed. • During RME. there won’t be enough receptors to handle it all. 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. • Instead.

and releases the contents of the vesicle outside the cell. lysosomes often break down wastes and other toxins inside the cell. • The vesicle is transported through the cytoplasm to fuse with the cell membrane.Exocytosis • Exocytosis uses vesicles to export large molecules out of the cell. . and these wastes are then transported out of the cell in a vesicle. opens. • This is useful for removing large waste particles. • For example. • The cell membrane rearranges.

One major problem with chemotherapy drugs is that they are not able to target just the cancer cells. These tissues can then be implanted into an organism to assist in the organism’s growth and repair. . they kill healthy cells as well.Cell Research in Medicine • Cancer cells reproduce in an abnormal manner. • 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. Cancer patients often undergo treatments such as chemotherapy to destroy the abnormal cancer cells.