Biology Unit 3 AoS1

8/13/2019 Biology Unit 3 AoS1

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THE NATURE AND IMPORTANCE OF

BIOMACROMOLECULES IN THE CHEMISTRY OF THE

CELL:

SYNTHESIS OF BIOMACROMOLECULES THROUGH THE CONDENSATION REACTION.

Biomacromolecules: a large organic molecule commonly created by the polymerisation of smaller sub-units; includes lipids,

carbohydrates, nucleic acids and proteins. They are synthesised through the condensation polymerisation reactions:

Polymer unit Monomer unit Bond Elements Polymerisation reaction

Nucleic acids Nucleotides Phosphodiester bond C, H, O, N, PCondensation reaction

water is produced in the

process.

Proteins Amino acids Peptide bond C, H, O, N

Polysaccharides Monosaccharides Glycosidic bond C, H, O

Lipids* Fatty acids, glycerol Ester bond C, H, O

*Note that lipids are not polymers; they are organic compounds composed of smaller sub-units.

o The breakdown of polymers into monomers is a hydrolysis reaction water is required as a reactant for the polymersto break down.

Organic compound: compound which contains both carbon and hydrogen.

Biomolecule: biologicallyimportant molecules present in cells, usually containing carbon, hydrogen and oxygen.

Polymer:a large molecule consisting of many identical repeating monomer units bonded together.

Monomer:a small molecule that canbebonded to other identical molecules to form a polymer.

LIPIDS AND THEIR SUB-UNITS; THE ROLE OF LIPIDS IN THE PLASMA MEMBRANE.

Lipids: general term for fats, waxes, oils; non-polar/hydrophobic/lipophilic substance largely made of molecules containing

carbon, hydrogen, oxygen and occasionally phosphorus and nitrogen.

Triglycerides

o Energy storage, e.g. in triglycerides. Lipids can hold more energy than the other biomacromolecules.o Structure, e.g. in plasma membranes.o Biological roles, as hormones, receptor sites, vitamins and co-enzymes.o Triglyceride moleculesare composed of three fatty acids and one glycerol.

- They contain very little water and carry a large amount of energy.- It is commonly used as a form of energy storage in animals.

Fat type Bonding infatty acid

Notes State atRT

Commonname

Examples

Saturated Single bond

Straight tail, are able to be packed

closely together. It takes more energy to

move molecules past one another.

SolidFats,

waxes

Cheese,

butter

Unsaturated

Mono-

unsaturated

One double

bondBent tail, are not able to be packed

closely together. It takes less energy to

move molecules past one another.

Liquid OilsOlive oil,

mayonnaisePoly-

unsaturated

Multiple

double bonds

Phospholipids

Phospholipids: major type of lipid found in plasma membranes; consists of a lipid attached to a phosphate group.

o Form a bilayer in plasma membranes, with the phosphate groups facing outwards and the fatty acids facing inwards.o Is an amphipathic molecule, i.e. hydrophilic phosphate head, hydrophobic fatty acid tails.


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EXAMPLES OF POLYSACCHARIDES AND THEIR GLUCOSE MONOMER.

Carbohydrates: organic compounds important as a structural component and energy source; made of carbon, hydrogen and

oxygen.

Carbohydrate Bond Formula Examples Functions

Simple

carbohydrates

(sugars)

Monosaccharide

Glycosidicbond

C6H12O6/

CnH2nOn

Glucose, fructose, ribose,

galactoseSource of energy

Disaccharide C12H22O11 Sucrose, lactose, maltose Transportation in plants

Complex

carbohydratesPolysaccharide -

Starch, cellulose, glycogen,

chitin, pectinEnergy storage, structure

Monosaccharides

o Simple carbohydrates (called sugars) are small and polar.o Most complex carbohydrates are non-polar.

- Some complex carbohydrates such as starch are used for energy storage.- Their presence in cell cytoplasm does not affect the concentration of solutes; thus they may be stored in cells

without affecting diffusion and osmosis.

o Many monosaccharideshave the same formula C6H12O6but different molecular structures; they are isomers.o Glucose: reactant in cellular respiration and is a fundamental unit for the formation of disaccharides and

polysaccharides.

Polysaccharides

Polysaccharides: complex carbohydrate polymers of sugar molecules, made by linking monosaccharides, usually glucose. A

glycosidic bond joins the monosaccharides. The following are examples of polysaccharides.

o Glycogen: form of energy storage in animals.- Structure: branching chains of sugars starting from a primer protein.- Excess glucose is taken to the liver to be converted into glycogen. When storage capacity of glycogen is reached,

excess glucose is converted to lipid storage.

o Starch: chief form of energy storage in most plants.- Structure: chains of glucose forming spiral-shaped grains.- Starch can be stored in modified stems, roots and leaves and seeds. It can also be readily converted back into

sugar.

- Inulin: storage polysaccharide of the general class of starches but formed from fructose; unlike starch, inulin iswater-soluble.


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o Cellulose:structural polysaccharide.- Structure: long and unbranched molecule, forms tough fibres ideal for their structural role.- All plant cell walls are composed of cellulose.- Pectin, another polysaccharide, is the material between cell walls of plant cells.- Chitin, a derivative of cellulose, is found in the exoskeletons of some insects such as flies.

STRUCTURE AND FUNCTION OF DNA, RNA, THEIR MONOMERS, AND COMPLEMENTARY BASE

PAIRING.

Genome: the complete set of genetic material of an organism.

Nucleic acids: organic compounds build from nucleotides; include DNA and RNA.

Nucleotides

o A nucleotideconsists of three main parts:- Sugar- Phosphate group- Nitrogenenous base

Purines: larger with double-ring structure. Includes adenine and guanine. Pyramidines: smaller with single-ring structure. Includes cytosine, thymine and uracil. Complementary pairs: adenine and uracil/thymine; guanine and cytosine

o Complementary nitrogenous pairs are involved in the formation of the DNA double helix, transcription and translation.o The phosphate group of one nucleotide joins to the sugar of another by a covalent phosphodiester bond, to form a

chain of nucleotides.

Nucleic acid P group SugarNitrogen bases

Purines Pyramadines

DNA Phosphate

group

Deoxyribose sugarAdenine Guanine Cytosine

Thymine

RNA Ribose sugar Uracil

DNA RNAExists as double-stranded molecule. Exists as single-stranded molecule.

May have thymine as a nitrogenous base. May have uracil as a nitrogenous base.

Found in the nucleus only.Some are formed in the nucleus; all may be found in the

cytoplasm.

DNA

Deoxyribose nucleic acid (DNA): nucleic acid which forms a major component of chromosomes, containing the code for proteinproduction.

o DNAis double-stranded.- Nitrogen bases of one strand are complementary to those of another strand of nucleotides.


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- Two strands join by hydrogen bonds between complementary nitrogen bases.- Forms a double-helix shaped molecule known as DNA.

o The two strands are anti-parallel; one strand is five prime (5') to three prime (3') whereas the other is 3' to 5'.o The DNA double helix combines with certain proteins to form a chromosome.

o Chromosomes are in the nucleus of the cell and never leave.o Contain genetic instructions for synthesis of proteins that control all the functions of the cell.

RNA

Ribose nucleic acid (RNA): nucleic acid which plays essential role in protein synthesis and as a structural component of

ribosomes.

RNA Description Function Produced in Notes

Messenger RNA

(mRNA)

A single stranded

copy of DNA.

Carry the code for protein

synthesis out of the nucleus

to the ribosomes.

Nucleus

The N-bases of mRNA are

complementary to the strand of

DNA from which it was produced.

The process of producing mRNA is

called transcription.

Ribosomal RNA

(rRNA)

Combines withproteins to form a

ribosome.

Translates mRNA andcreates a chain of amino

acids.

NucleolusAmino acids are joined during

translation to form a polymer. This is

the primary structure of a protein.

Transfer RNA

(tRNA)

Transportation

RNA.

Carries a specific amino acid

to the ribosome during

protein synthesis.

- -

o DNA carries information for protein synthesis through nitrogen bases.o RNA is involved in taking the DNA code and synthesising actual proteins.o Code operates with every three nitrogen bases. The combination of the three determines the amino acid that will be

used. This topic will be explored in more detail later in the course.

o Thus in a mutated DNA, in which the nitrogen bases are out of order, the wrong protein will be produced.THE NATURE OF THE PROTEOME; THE FUNCTIONAL DIVERSITY OF PROTEINS; THE STRUCTURE OF

PROTEINS IN TERMS OF PRIMARY, SECONDARY, TERTIARY AND QUATERNARY LEVELS OF

ORGANISATION.

Proteins: biologically functional organic compounds build of one or more amino acid chains coiled into specific 3D structures.

o Very large molecules containing carbon, hydrogen, oxygen and nitrogen; some also contain sulphur and phosphorus.o They are a very diverse group of molecules in terms of function.

Proteome: the complete array of proteins produced by a particular genome.

o In living organisms, proteins are involved in virtually every chemical reaction.o May be enzymes, reactants, products, or all three.o Proteomics is studied because no protein acts in isolation from other proteins.

Type of protein Function Example

StructuralFibrous support tissue in skin, bone, tendons, cartilage, blood

vessels, heart valves and cornea of the eye. Nails, hair.Collagen, keratin.

Enzyme Catalyse biochemical reactions. Amylase, pepsin, catalase.

Contractile Muscle movement. Myosin, actin.

Immunoglobulin Defence against disease. Antibodies.

Hormone Regulate body activity. Insulin, oestrogen, adrenaline.

Receptor Respond to stimuli. Insulin receptors.

Transport Transport of other molecules. Haemoglobin, carrier proteins.


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Amino acids

o Amino acidsare the monomers of proteins.o 20 naturally occurring amino acids.o Different proteins contain different numbers and

proportions of amino acids.

o An amino acid is structured like the diagram to theright; the R group varies in every different amino acid.

Polypeptides and protein structure

o A peptide bond forms between the amino group of one and the carboxyl group of another, and a water molecule isreleased to form a dipeptide. A long chain of amino acids joined is a polypeptide.

o Each type of protein has a specific linear sequence of amino acids.o The chain of amino acids then can fold in different ways depending on their purpose.o A protein can become functional in its tertiary structure. This is because not all proteins have a quaternary structure.

Primary structure:the specific linear sequence of amino acids in a protein. Determined by the mRNA template from which the

polypeptide is built.

Secondary structure:regions of folding of coiling of a protein polypeptide chain due to hydrogen bonding. The polypeptide can

adopt more than one fold.

o Alpha () helices are a spiral/coil shape formed byhydrogen bonding between different amino acids; this

causes the peptide chain to coil.

- Elastic. When stretched, the hydrogenbonds break; they reform when the fibre is let go.

- Hair and wool keratin proteins tend to havemany alpha helices.

o Beta () pleated sheets are folded sheets thatcannot be further stretched. Part of the peptide chain fold

back on each other, forming hydrogen bonds between

neighbouring amino acids.

- Silk fibroin proteins have many betapleated sheets.

o Random coilsare folded parts of the peptide chainthat appear to have no set shape or structure; however,

proteins of the same type have identical random coils.

- The random coils often have specificbinding sites where other molecules may link.

- The random coil is often the most activesite of the protein.

Tertiary structure: the total irregular folding of the peptide

chain to become a complex shape.The bonds form between

side chains of amino acids and form a complex structure. The

shape of the tertiary structure is important to the function of

the protein. Many proteins are functional at this stage. Most

enzymes possess a tertiary structure.

o Hydrogen bonding between the R groups.o Ionic bonding between the R groups.

o Covalent bonding between the sulphur atoms of the R groups, forming disulphide bonds.o Hydrophobic interactions between R groups, causing them to collect in the centre of the protein.


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Quaternary structure: particular shape of a complex protein which consists of more than one polypeptide subunits. The

quaternary structure results in a globular structure, e.g. haemoglobin, or fibrous structure, e.g. collagen.

o Insulin: protein hormone with a quaternary structure.- Initially inactive as a hormone; it is a single chain of amino acids.- An enzyme cuts the amino acid chain, leaving two chains of amino acids held together by disulphide bonds. This

results in an active protein with a quaternary structure.

o Polypeptides can also join with other types of biomolecules to form conjugated proteins, as compared to simpleproteins, which only contain amino acids.

- Glycoproteins (contain carbohydrates), lipoproteins (contain lipids), nucleoproteins (contain nucleic acids) etc.Haemoglobin is another example of a conjugated protein, it contains carbohydrates.

Denaturation of proteins

Denaturation: change in the secondary and/or tertiary structure of a protein and thus change in 3D structure; often irreversible.

Conditions Reason Structures affected

pH (strong acids

or alkalis)

The hydrogen or hydroxide ions present in strong acids or

alkalis disrupt ionic bonds in the protein.

Secondary and tertiary structures.

Extended exposure can affect primary

structure.

Heat and

radiation

Can break some of the bonds in the protein due to atoms

moving more as a result of energy provided to atoms.Secondary and tertiary structures.

Heavy metalsMay disrupt ionic bonds and form strong bonds with the

carboxyl groups, reducing the protein charge.Secondary and tertiary structures.

Detergents and

solvents

These substances form bonds with the non-polar groups, and

can disrupt hydrogen bonding and hydrophobic interactions.Tertiary structures.


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THE STRUCTURE AND FUNCTION OF THE PLASMA

MEMBRANE AND THE MOVEMENT OF SUBSTANCES

ACROSS IT:

THE FLUID-MOSAIC MODEL OF A PLASMA MEMBRANE

Fluid mosaic model: the current model used to describe the structure of the plasma membrane. "Fluid" refers to the ability of

the membrane to move fluidly. "Mosaic" refers to the array of molecules present in the membrane.

"Mosaic"

o Phospholipid bilayer: phospholipids are amphipathic.- Hydrophobic fatty acids repel most hydrophilic substances.

o Glycolipids: phospholipids with carbohydrates attached to them.- Act as surface receptors for signalling molecules such as hormones.- Also play a role in helping cells aggregate to form tissues.

o Proteins are embedded in the bilayer.- Transmembrane proteins are often protein channels which are involved in the movement of substances in and

out of the cell.

- Some proteins may also be enzymes that catalyse membrane-associated reactions.o Glycoproteins: proteins with a carbohydrate attached to them.

- Antigens are glycoproteins that allow the organism to recognise "self" or "non-self". This allows the immunesystem to detect foreign cells.

"Fluid"

o

Cholesterol is embedded in the bilayer, gives stability and prevents the membrane from becoming too rigid. Movementof the membrane is thus more fluid.

THE PACKAGING, TRANSPORT, IMPORT AND EXPORT OF BIOMACROMOLECULES (SPECIFICALLY

PROTEINS).


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Type of

transport

Cell components

involvedTypes of substances transported Examples of substances transported

Diffusion Phospholipid bilayerSmall, uncharged and/or lipophilic

molecules.Water, oxygen, alcohol, urea.

Facilitated

diffusion

Protein channels, carrier

proteinsCharged and/or polar molecules.

Glucose, water, fructose, hydrogen

ions.

Active

transportCarrier proteins Charged and/or polar molecules.

Glucose, water, fructose, hydrogen

ions.

Endocytosis/exocytosis

Phospholipid bilayer,

vesiclesLarge and/or polar molecules. Proteins, starch, macromolecules.

Passive transport

Concentration gradient: the difference of solute concentration between two areas.

Diffusion: the passive net movement of solutes from an area of high solute concentration to one of low solute concentration.

o All cells must be able to exchange materials with its environment to survive, grow and reproduce.o The plasma membrane only allows certain substances across it; hence it is semi-permeable.o Substances that cannot directly cross the plasma membrane must enter or exit the cell by other means.o Substances that can diffuse directly across the plasma membrane include:

- Lipophilic substances of various sizes, e.g. alcohol and chlorofoam, can dissolve into the phospholipid bilayer,and thus pass through the plasma membrane.

- Very small molecules, e.g. water and urea, can pass between the phospholipid molecules of the plasmamembrane.

- Small, uncharged molecules, e.g. oxygen and carbon dioxide, can pass directly through the phospholipid bilayer.Facilitated diffusion: passive diffusion which occurs through transport proteins in a cell membrane from an area of high solute

concentration to one of low solute concentration.

o Substances that cannot diffuse directly through the plasma membrane may diffuse through the transmembranetransport proteins.

o These proteins are specific to the molecules or group of molecules they transport and can become saturated. This mayinhibit the movement of other molecules.

- Hydrophilic protein channels act as a tunnel through which certain molecules can move through. These tunnelscan be opened or closed.

- Carrier proteins take the transported substance and changes shape in a way that carries the substance acrossthe membrane.

o Sometimes a carrier molecule is needed for facilitated diffusion to occur. An example of this is glucose; for glucose tomove across the membrane of red blood cells, a specific carrier molecule is required.

Osmosis: the passive net movement of water across a semi-permeable membrane from an area of low solute concentration to

one of high solute concentration.Osmotic pressure:the pressure that causes osmosis.

Hypotonic:a solution that has a lower solute concentration than the cells which it contains. Animal cells take in water and swell,

and may burst, i.e. cytolysis. Plant cells do not burst due to the support of the cell wall, they become turgid.

Isotonic:a solution that has the same solute concentration as the cells which it contains. Cells do not change.

Hypertonic:a solution that has a higher solute concentration than the cells which it contains. Animal cells lose water and shrink

and shrivel, i.e. crenation. Plant cells become flaccid, i.e. undergone plasmolysis.

o Excess water taken in by the cell moves into the vacuole; once they are full, they fuse with the cell membrane and expelthe water. This prevents the cell from bursting.

Active transport

Active transport:net movement of solutes across a cell membrane through an energy-expending process from an area of low

solute concentration to one of high solute concentration.


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o When substances need to be moved against the concentration gradient, a cell must expend energy in the form of ATPto do so.

o Active transport can be through carrier proteins or through endocytosis or exocytosis if the molecules are needed inbulk or very large.

Endocytosis: bulk movement of a substance into a cell by engulfment.

Exocytosis: movement of a substance out of a cell through vesicles merging with the cell membrane.

Pinocytosis: bulk movement of liquid into a cell by engulfment.

Phagocytosis: bulk movement of solid material into a cell by engulfment.

o Endocytosis: the cell surrounds the substance and folds inwards. A part of the cell membrane pinches off and forms avesicle in the cytoplasm, containing the substance.

- Receptor-mediated endocytosis: when a specific molecule binds to a receptor of a specific area of the cellmembrane, the cell acknowledges the signal and endocytosis is activated, thus taking in the substance.

o Exocytosis: a vesicle containing the substance merges with the cell membrane and expels its contents.THE ROLE PLAYED BY ORGANELLES INCLUDING RIBOSOMES, ENDOPLASMIC RETICULUM, GOLGI

APPARATUS AND ASSOCIATED VESICLES IN THE EXPORT OF PROTEINS.

Ribosomes: an organelle of rRNA and protein that functions as a site of protein synthesis.Endoplasmic reticulum (ER): eukaryotic organelle that is a system of membranous channels which are involve intracellular

transport of materials; the rough ER is embedded with ribosomes and mainly involved in packaging and transport of proteins;

the smooth ER is mainly involved in synthesis of lipids and detoxification of drugs and poisons.

Golgi apparatus: eukaryotic organelle that is a stack of flattened membrane sacs and is involved in the sorting, packaging and

storage of lipids and proteins and the movement of these materials via vesicles.

The steps of protein synthesis are briefly explained below:

1. Transcription: doubled-stranded DNA unwinds into a single strand, and a complementary mRNA is synthesised in thenucleus. mRNA then moves into the cell cytoplasm.

2. Translation: mRNA moves to a ribosome, where the code of the mRNA is translated into an amino acid chain by theribosome.

- Ribosomes are usually free-floating in the cytosol.- If a ribosome begins synthesising a protein needed outside the cell, it embeds itself to the ER.- If the protein is needed locally, the ribosome remains in the cytosol.

3. The code of mRNA is read through the nitrogen bases, three at a time.- Three simultaneous nitrogen bases are called a codon; the combination of different nitrogen bases in a codon

determines a particular amino acid to be added to the chain.

4. tRNA carries the required amino acid to the ribosomes.- The tRNA contains a part called the anticodon; the anticodon consists of three nitrogen bases which is

complementary to a particular codon.

- Thus only a specific tRNA can line up with a specific codon to provide the specified amino acid.5. The ribosome moves along the mRNA strand, collecting amino acids along the way and thus building the polypeptide

chain.

6. At the end of the mRNA there is a stop codon, which signals the ribosome to finish the chain of amino acids. In thecase of proteins needed outside the cell, the amino acid chain is released to the endoplasmic reticulum in a small

vesicle for packaging and transport.

7. In the ER, the amino acid chain is folded and given its secondary, tertiary and occasionally quaternary structure.8. The protein is then released to the Golgi apparatus, where it may have other biomolecules added to it, and then sent

via a vesicle to the cell membrane, where it will be secreted by exocytosis.

9. Proteins created by cytoplasmic ribosomes are released when they are completed and move to parts of the cell wherethey are required.


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THE NATURE OF BIOCHEMICAL PROCESSES WITHIN

CELLS:

CATABOLIC AND ANABOLIC REACTIONS IN TERMS OF REACTIONS THAT RELEASE OR REQUIRE

ENERGY.

Catabolic: describing a chemical reaction in which larger molecules are broken down into smaller sub-units; commonlyexergonic reactions.

Exergonic:describing a chemical reaction which releases energy.

Anabolic:describing a chemical reaction in which smaller sub-units are joined to form larger molecules; commonly endergonic

reactions.

Endergonic:describing a chemical reaction which requires energy to proceed.

Type of

reactionExample

Anabolic/

Endergonic

Reduction reactions, which involve the removal of oxygen or the addition of

electrons to a substance.

The Calvin cycle involves the reduction of intermediate 3 carbon molecules.

Condensation polymerisation

reactions.

Formation of proteins in ribosomes.

Catabolic/

Exergonic

Oxidation reactions, which involve the addition of oxygen or the removal of

electrons from a substance.

Respiration involves the oxidation of sugars into carbon dioxide and water.

Hydrolysis reactions.

Breakdown of proteins into amino

acids by digestive enzymes.

About redox reactions and exergonic/endergonic reactions:

o Energy is required to take an electron from an atom. The more electronegative an atom, the more energy is required to take an electron away. An electron loses potential energy when it moves from an atom of lower electronegativity to one of higher

electronegativity.

Thus when an oxidation reaction occurs, i.e. causing electrons to lose potential energy, energy is released.o Oxygen atoms are very electronegative.

Thus if oxygen is added to a molecule, electrons are moved to the oxygen, resulting in release of energy.THE ROLE OF ENZYMES AS PROTEIN CATALYSTS, THEIR MODE OF ACTION AND THE INHIBITION OF

THE ACTION OF ENZYMES BOTH NATURALLY AND BY RATIONAL DRUG DESIGN.

Enzymes: a specific protein that acts as a catalyst to increase the rate of a particular chemical reaction without being consumed

in the process.

o Chemical reactions can only occur if there is sufficient energyavailable.

The energy required to start a reaction is calledactivation energy.

Activation energy is usually supplied in the form ofthermal energy from the environment.

However, in most cases, the activation energy is so highthat the reaction would hardly proceed at room

temperature.

o Enzymes reduce the activation energy needed for a particularreaction. Hence, the rate of reaction will increase.

o Without enzymes, metabolism would be too slow to providesufficient energy to maintain life.

Structure and mode of action of enzymes

Active site: specific region of an enzyme that binds with the substrate.


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Substrate: reactant on which an enzyme works.

Enzyme-substrate complex: a temporary complex formed when an enzyme binds to its substrate(s).

o Enzymes are made mainly of tertiary proteins.o Enzymes are highly specific; each type of enzyme acts on only one type of substrate.

e.g. Maltase will only act on maltose but not sucrose, even though both are disaccharides.o The specificity of an enzymeis due to the need for a complementary fit between the shapes of the enzyme's active site

and its substrate.

Cofactors: any non-protein molecule or ion that is needed for the proper functioning of an enzyme.

Coenzymes: any organic molecule serving as a cofactor.

o Cofactors include coenzymes.o Cofactors may be prosthetic groups, which are bound permanently to the enzyme.o They may also bind loosely and reversibly only during catalysis.o Common cofactors are metal ions, e.g. Ca2+, Zn2+, etc.o Common coenzymes are vitamins.

Induced fit model: the active site of the enzyme is shaped similarly to the substrate. The entry of the substrate into the enzyme

causes a change in the active site of the enzyme, creating a complementary fit. Currently accepted model for enzyme-substratebinding.

Lock and key model: the enzyme and substrate possess perfectly complementary shapes that fit exactly into one another like a

key into a lock.

Factors affecting enzyme activity

Temperature

o Enzymes are temperature sensitive.o They have an optimum temperature at which enzyme activity is most efficient.

Animals: around body temperature (37C). Plants: around 28C-35C. Thermophilic bacteria: around 70C.

o If the temperature deviates too far from the optimum temperature, theenzyme will denature.

Heat increases movement of atoms; if atoms become agitated, weakbonds within the enzyme can break.

Heat can affect the secondary and tertiary structures of enzyme.


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pH

o Enzymes are also pH sensitive.o There is an optimum pH for the most efficient functioning of an enzyme.

Generally, enzymes operate well at around pH7 (i.e.neutral), withthe exception of some enzymes, such as digestive enzymes.

Digestive enzymes are adapted to withstand the acidic environmentin which they work.

o If the pH deviates too far from the optimum pH, the enzyme will denature. In highly acidic or alkaline solutions, there is an abundance of

hydrogen or hydroxide ions.

These ions will disrupt ionic bonding and thus the tertiary structure ofthe enzyme.

Concentration of enzymes

o If the concentration of enzymes increases whilst other variables remainconstant, the rate of reaction increases.

o This is because there are more enzymes available to catalyse the reaction.o However, the concentration of substrates can be limiting; if all of the

substrates are converted to products, there will be no more substrate left to

convert and thus the reaction ceases.

Concentration of substrates

o If the concentration of substrates increases whilst other variables remainconstant, the rate of reaction increases.

o This is because substrates will not limit the rate of reaction and also ensurethat more enzymes are working at a time.

o However, the concentration of enzymes can be limiting; once all of the activesites of enzymes become occupied, the rate of reaction will plateau no matter

how much more substrates are added.

Enzyme inhibition

Enzyme inhibitors: chemicals that bind to enzymes and decrease their activity.

o If the inhibitor binds to the enzyme by covalent (i.e. strong) bonds, inhibition is usually irreversible.o Inhibition occurs both naturally and also as a result of toxins/drugs.

Inhibition type

Drugs Naturally

Competitive inhibition

If a person ingests ethylene glycol, it will be broken down by

the enzyme alcohol dehyrogenase (ADH) into the poisonous

oxalic acid. Alcohol can be ingested to treat this, as it is a

competitive inhibitor for ADH and prevents the ADH from

breaking down ethylene glycol, which is then excreted.

Irreversible non-competitive inhibition

Heavy metals such as arsenic, mercury and lead, affect the

tertiary structures of enzymes and change the shape of the

active site. This will eventually be fatal to the organism as

enzymes will no longer catalyse important reactions, and

metabolism would become too slow to maintain life.

Irreversible competitive inhibition

Penicillin permanently and competitively inhibits the bacterial

enzyme transpeptidase, which prevents bacterial cell walls

from forming.

Reversible inhibition

The final product in a biochemical pathway can inhibit

intermediate enzymes. This slows down the pathway,

ensuring that the final product will not be accumulated.

o Competitive inhibition Inhibitors mimic the shape of the substrates and thus compete with substrate to bind to the active site of the

enzyme.


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This inhibits the activity of enzymes by preventing enzymes from binding with substrates. Inhibitor usually binds by weak interactions (i.e. usually reversible).

o Non-competitive inhibition Inhibitors bind to an area of the enzyme that is not the active site, and slightly its shape in the process. The enzyme thus loses its specificity of shape and cannot bind with substrates as efficiently as before. Thus enzyme activity is reduced due to difficulty binding with substrates.

o Allosteric inhibition Inhibitors bind to an area of the enzyme that is not the active site, and distort its shape. The enzyme completely loses its specificity of shape and cannot bind to substrates at all. Thus enzyme activity ceases.

Rational drug design

Rational drug design: construction of a drug to fit the active site of a molecule so that the natural action of the molecule cannot

occur. The process involves finding out how the infective agent works against a cell and using that information to tailor a drug

that prevents the infective agent from doing this.

o AZT (azidothymidine): inhibits HIV-1 reverse transcriptase to treat HIV/AIDS.o Influenza: viruses are constantly changing into new strains, as the proteins in their outer layer continually change.

Thus a person can get influenza multiple times in their life. Rational drug design has improved treatment for prevention of influenza: There are two kinds of protein on the surface of the virus.

Haemagglutinin is involved in the virus gaining entry into the cell. Neuraminidase is involved in the virus leaving the cell to infect other cells.


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It was found that the active site of neuraminidase remained constant in different strains. Thus neuraminidase can be targeted by rational drug design to stop the progression of influenza. Anti-influenza drugs were designed to have a complementary shape to the active site of neuraminidase. They

can thus inhibit neuraminidase and prevent it from carrying out its function, i.e. allow virus to leave the cell

and infect other cells.

Thus the virus will remain attached to the cell until the bodys immune system identifies it and takes care of it.

o PKU: phenylketonuria. The enzyme phenylalanine hydroxylase cannot be produced. Phenylalanine hydroxylase usually breaks down phenylalanine into tyrosine. Without it, phenylalanine cannot

be broken down.

The build-up of phenylalanine in brain tissue causes brain damage and can result in death. Early detection of PKU is vital so that the affected person can avoid eating foods with very low amounts of

phenylalanine.

oTHE ROLE OF ATP AND ADP IN ENERGY TRANSFORMATIONS.

ATP: adenosine triphosphate, a nucleotide that releases free energy when broken down into ADP and inorganic phosphate. It is

the form of energy that drives all metabolic processes in cells.

ADP: adenosine triphosphate, a nucleotide which is the product of ATP hydrolysis. An inorganic phosphate can be added to it to

form ATP.

o Cells couple exergonic reactions to drive endergonic reactions. In most cases the hydrolysis of ATP is the exergonicreaction.

o When the terminal phosphate bond of ATP is broken by addition of a water molecule, a large amount of energy isreleased, leaving ADP and inorganic phosphate.

o ADP can be "recharged" by the addition of an inorganic phosphate to ADP using energy (i.e. endergonic).o Usually this is done through cellular respiration, in which organic compounds are broken down to release energy.


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REQUIREMENTS FOR PHOTOSYNTHESIS EXCLUDING DIFFERENCES BETWEEN CAM, C3 AND C4

PLANTSINCLUDING: THE STRUCTURE AND FUNCTION OF THE CHLOROPLAST; THE MAIN INPUTS

AND OUTPUTS OF THE LIGHT DEPENDENT AND LIGHT INDEPENDENT STAGES.

Photosynthesis: the conversion of light energy to chemical energy, which is stored in organic compounds, usually sugars. Occurs

in plants, algae and certain prokaryotes.

o The sun is the ultimate source of energy.o Photosynthetic organisms can harness this energy to synthesise organic molecules. They are also called producers.o The pigment required to trap sunlight can not only be chlorophyll, but other pigments depending on the organism.

Carotenoid is another example of a photosynthetic pigment.o Chlorophyll absorbs red and blue light the most; thus photosynthesis is more efficient in red or blue light.

This is because chlorophyll reflects green light, as it is green itself. Thus the green light cannot be absorbed andused in photosynthesis.

o Rate is affected by: light intensity, concentration of carbon dioxide, water availability, temperature.o In plants, the overall process of photosynthesis can be summarised as:Carbon dioxide + water ------------------------> glucose + oxygen

6CO2+ 12H2O ------------------------> C6H12O6+ 6O2+ 6H2O

o Photosynthesis is in fact a very complex process that isgenerally split into two main stages: the light-dependent

stage and the light independent stage (carbon reduction).

Stage of photosynthesis Light dependent Light independent

Location Thylakoids ofchloroplasts

Matrix ofchloroplasts

Type of reaction Catabolic Anabolic

The chloroplast

o The chloroplast is the site of photosynthesis in plants.o They are found in any green part of a plant, mostly in mesophyll cells in leaves.o Structure of the chloroplast:

Double membrane containing a dense fluid called the stroma Inside the stroma, membranous sacs called thylakoids are organised into stacks called grana (singular granum) Chlorophyll is contained in the thylakoids The enzymes involved in photosynthesis can be found in the stroma and grana membranes.

light and chlorophyll

light and chlorophyll


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o The chloroplast also contains its own DNA and ribosomes for protein synthesis. This can be explained by theory of endosymbiosis, which suggests that the chloroplast was once an organism

that was engulfed by another cell, forming the double membrane of the chloroplast. The two organisms lived

symbiotically and became one organism.

Light-dependent stage of photosynthesis

o The first stage of photosynthesis is light-dependent andcatabolic/exergonic.

o It uses light energy to generate ATP and NADPH from thesplitting of water molecules.

o Location: grana of thylakoids in the chloroplasts.o Inputs: sunlight energy, 12H2O, 2ADP+2Pi, 24NADPo Outputs: 6O2, 2 ATP, 24 NADPHo The steps of the light-dependent stage are as follows:1. The light energy absorbed by chlorophyll help break the

water into oxygen and hydrogen.

Oxygen is released into the atmosphere.2. Electron transfer reactions provide energy for the

formation of ATP and NADPH

Light-independent stage of photosynthesis

o The second stage of photosynthesis is light-independent and anabolic/endergonic.

o It involves the Calvin cycle, a cyclic processof carbon fixation; carbon is reduced from

carbon dioxide to sugar.

NADPH and ATP from the lightdependent stage supply the energy

required to drive this reaction.

NADPH (reducing agent) providethe hydrogen ions required.

o Location: stroma of the chloroplasts.o Inputs: 24 NADPH, 6CO2, ATPo Outputs: 24 NADP, 2 phosphoglyceraldehyde, 6H2O, ADP, Pio The steps of the Calvin cycle are as follows:1. Carbon fixation: carbon dioxide incorporated into an organic molecule.

Three carbon dioxide molecules each join with a 5-C molecule (ribulose biphosphate, RuBP), then splits into two3-carbon molecules each.

3CO2 3 5-C molecules 6 3-C molecules2. Carbon reduction.


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Using ATP and NADPH, one phosphoglyceraldehyde is reduced from one of the 3-C molecules (reduction).3. Regeneration of RuBP: remaining 3-C molecules rest are converted back to the starter 5-C molecule using ATP and

returned to the cycle.

The Calvin cycle is a cycle because the end product ribulose biphosphate, a 5-C molecule, is used to start thereaction again, i.e. one of the end products is also a starting reactant, hence the series of reactions replenishes

its own resources.

The cycle repeats, producing one another phosphoglyceraldehyde from the other three carbon dioxidemolecules.

4. The two phosphoglyceraldehyde enter the cytosol of the plant cell, where they under reactions to form one glucosemolecule.

5. Leftover hydrogen ions combine with oxygen to produce water.

REQUIREMENTS FOR AEROBIC AND ANAEROBIC CELLULAR RESPIRATION: THE LOCATION, AND

MAIN INPUTS AND OUTPUTS, OF GLYCOLYSIS; THE STRUCTURE OF THE MITOCHONDRION AND ITS

FUNCTION IN AEROBIC CELLULAR RESPIRATION INCLUDING MAIN INPUTS AND OUTPUTS OF THE

KREBS CYCLE AND THE ELECTRON TRANSPORT CHAIN.

Cellular respiration: series of exergonic reactions that break down organic compounds, releasing energy and transferring it to

ATP.

o Organisms must transfer the energy in glucose to ATP before it can be used, i.e. cellular respiration. Glucose is broken down, releasing energy. Some energy is used to convert ADP and inorganic phosphate to ATP. The remainder energy is lost as heat energy, which cannot be used for energy-requiring activities.


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o Cellular respiration occurs all the time in the cells of all living things.o Glucose is the most commonly used molecule for cellular respiration.

When the body runs out of glucose andglycogen, fat is converted to glucose for

respiration.

Other organic molecules can also be used incellular respiration.

o Glycolysis is the first stage of cellular respiration. In the presence of oxygen, respiration

proceeds down an aerobic pathway.

If oxygen is insufficient, respiration proceedsdown an anaerobic pathway.

o Aerobic cellular respiration can be summarised in the following equation:Glucose + oxygen ------> carbon dioxide + water + energy

C6H12O6+ 6O2------> 6CO2+ 6H2O + energy (ATP + heat)

o Some organisms living in extreme conditions constantly rely on anaerobic respiration.

Stage of respiration Glycolysis Anaerobic pathwayAerobic pathway

Krebs cycle Electron transport chain

Location Cytosol Cytosol Matrix of mitochondria Cristae of mitochondria

Type of reaction Catabolic - Catabolic

ProcessGlucose broken down

into pyruvate.

Pyruvate broken down

into smaller organic

molecules, e.g. lactate.

Series of reactions

producing carbon

dioxide, ATP and

hydrogen.

Hydrogen is oxidised to

water. Energy is

released as ATP.

o Glucose is not the only organic compound that can undergo respiration.o Other biomolecules can also enter the respiration pathway.o When glucose is not available, fats and then protein are used.

The brain, heart and diaphragm are not affected.


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The mitochondrion

o Mitochondria are the site for aerobic respiration in eukaryotic cells.o In the presence of oxygen, they convert energy in organic molecules

into ATP.

o The structure of the mitochondrion: Double membrane Highly folded inner membrane, called the cristae.

Has proteins embedded in it needed for the electrontransport chain.

Has a large surface area for reactions to occur. The space between the inner and outer membranes is called

the intermembrane space.

Contains fluid called the matrix. Contains DNA and ribosomes.

o It is thought that like the chloroplast, the mitochondrion was a result of endosymbiosis.Glycolysis

Glycolysis: series of reactions that ultimately split glucose into pyruvate. Starting point for fermentation or respiration.

o Glycolysis involves the breakdown of glucose into two pyruvate with the release of 2 ATP.o Location: cytoplasmo Inputs: C6H12O6, 2ATP, 2ADP+2Pi, 2NAD+o Outputs: 2 pyruvate, 2NADH, 4ATPo The steps of glycolysis are as follows:1. Using 2 ATP, glucose is phosphorylised (i.e. have phosphate attached to),

becoming a 6-C glucose phosphate.

2. The 6-C glucose phosphate breaks into two 3-C sugar phosphates.3. Each 3-C sugar phosphate breaks into a 3-C pyruvate, giving off 2 ATP in the

process.

4. When glucose is broken down, hydrogen atoms are removed from glucose. Thehydrogen atoms and their electrons are picked up by NAD acceptor molecules.

5. Thus there are 4 ATP produced in glycolysis, resulting in a net yield of 2 ATP.Aerobic respiration

Aerobic respiration: breakdown of glucose into simple inorganic compounds in the presence of oxygen, with the release of

energy that transferred to ATP.

Krebs cycle: also known as the citric acid cycle, it is the second stage of aerobic respiration, occurring mainly in the

mitochondria, in which pyruvate is broken down to carbon dioxide.

o Location: matrix of the mitochondria.o Inputs: 2 pyruvate, 8NAD+, 2FAD, 2ADP+2Pio Outputs: 6CO2, 8NADH, 2FADH2, 2ATPo The steps of the Krebs cycle are as follows:1. One 3-C pyruvate is converted to one 2-C acetyl CoA,

giving off one carbon dioxide in the process and

reducing NAD+to NADH.

2. Acetyl CoA enters the cycle and combines with the 4-C oxaloacetate to form the 6-C citrate.3. Citrate then continues in a series of chemical reactions, forming a number of intermediate products, and reducing NAD +

and FAD carriers to form NADH and FADH2, also releasing one ATP and two carbon dioxide per molecule of pyruvate.

4. The intermediate molecule malate is oxidised, reducing another NAD+and becoming oxaloacetate.5. Oxaloacetate can now combine with another acetyl CoA to continue another cycle.


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Electron transport chain: third stage of aerobic respiration, in which cytochromes transfer

electrons to be finally added to oxygen; energy released results in a major yield of ATP.

o Location: inner cristae membrane of mitochondria.o Inputs: NADH, FADH2, 6O2, 32ADP+32Pio Outputs: NAD+, FAD, 6H2O, 32ATPo The steps of the electron transport chain are as follows:1. Loaded acceptor molecules unload hydrogen through cytochromes embedded in the

cristae membrane. Electrons are left inside the cytochrome and the hydrogen ions move

through to the intermembrane space of the mitochondrion.

2. Electrons are transferred from one cytochrome to the next; releasing energy. The movement of the electrons power the movement of hydrogen ions

against the concentration gradient.

3. When the electrons reach the last cytochrome in the chain, the electrons are passedon to oxygen, the final electron acceptor, which then combined with the hydrogen ions to form

water.

4. Hydrogen ions in the intermembrane space move back into the matrix via ATPsynthase, an enzyme embedded in the cristae.

The movement of the hydrogen ions allow the enzyme to synthesise ATP.


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Anaerobic respiration

Anaerobic respiration: form of respiration occurring in the absence of oxygen, in which glucose is broken down into smaller

compounds, with release of energy that is transferred to ATP.

o The final product of anaerobic respiration varies in different organisms, depending on the enzymes that they posess. Humans: lactate. Plants and yeasts: ethanol and carbon dioxide.

o Anaerobic respiration allows organisms to continue functioning under conditions without oxygen or live in habitatswithout oxygen.

o The steps of anaerobic respiration are as follows:1. Glycolysis still occurs in the cytoplasm.2. In the absence of oxygen, pyruvate is converted to lactate in humans and ethanol and carbon dioxide in plants and

yeasts.

Lactate causes sore muscles in humans. If ethanol accumulates in plant or yeast cells, it becomes toxic.

3. When oxygen supply is adequate again, lactate is converted back to pyruvate and goes down an aerobic pathway.However, ethanol cannot be converted back to pyruvate in plants.

Lactate fermentation Ethanol fermentation

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Biology Unit 3 AoS1