The chemical The chemical nature of cellsnature of cells

(all that tricky chemistry stuff!!!)(all that tricky chemistry stuff!!!)

IntroductionIntroduction

At the most basic level, the cell is a highly At the most basic level, the cell is a highly organised assemblage of atoms organised assemblage of atoms interacting with each other in a myriad of interacting with each other in a myriad of chemical reactions.chemical reactions.

In order to understand the molecular In order to understand the molecular nature of the cell, we need to revisit some nature of the cell, we need to revisit some chemical concepts.chemical concepts.

Some definitionsSome definitions MatterMatter

Anything that takes up space and has mass.Anything that takes up space and has mass.

AtomAtom An atom a fundamental piece of matter. Everything in the An atom a fundamental piece of matter. Everything in the

universe (except energy) is made of matter, and, so, everything universe (except energy) is made of matter, and, so, everything in the universe is made of atoms. in the universe is made of atoms.

An atom itself is made up of three tiny kinds of particles called An atom itself is made up of three tiny kinds of particles called subatomic particles: protons, neutrons, and electrons.subatomic particles: protons, neutrons, and electrons.

IsotopeIsotope Different forms of atoms of the same element. They have the Different forms of atoms of the same element. They have the

same number of protons in their nuclei but a different number of same number of protons in their nuclei but a different number of neutrons. neutrons.

Some more definitionsSome more definitions MoleculeMolecule

Formed when two or more atoms are joined Formed when two or more atoms are joined chemically.chemically.

ElementElement An element is a substance consisting of only one type An element is a substance consisting of only one type

of atom. e.g oxygen gas is Oof atom. e.g oxygen gas is O22 (pairs of oxygen (pairs of oxygen atoms combine to give oxygen gas)atoms combine to give oxygen gas)

CompoundCompound A compound is a molecule that contains at least two A compound is a molecule that contains at least two

different types of molecules. e.g. water is Hdifferent types of molecules. e.g. water is H22O (two O (two hydrogens and one oxygen)hydrogens and one oxygen)

More about elementsMore about elements

There are 92 naturally occurring elements.There are 92 naturally occurring elements. Only 11 of these are found in organisms in Only 11 of these are found in organisms in

more than trace amounts, and four of more than trace amounts, and four of these make up more than 99% of these make up more than 99% of organisms by weight.organisms by weight.

The four most common elements in living The four most common elements in living organisms are carbon (C), hydrogen (H), organisms are carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).oxygen (O) and nitrogen (N).

Memory Aid!!!Memory Aid!!!

Most common elements:Most common elements:

CHONPSCHONPS C for carbonC for carbon H for hydrogenH for hydrogen O for oxygenO for oxygen N for nitrogenN for nitrogen P for phosphorousP for phosphorous S for sulfurS for sulfur

More about atomsMore about atoms The red and green The red and green

circles in the centre circles in the centre are the are the protonproton and and neutronneutron, they both , they both make up the nucleus.make up the nucleus.

The blue circle is the The blue circle is the electronelectron and the black and the black ring shows its orbit ring shows its orbit around the nucleus.around the nucleus.

Even more about atoms – particularly Even more about atoms – particularly electrons and electron shellselectrons and electron shells

The orbit or region of space around the nucleus in which The orbit or region of space around the nucleus in which electrons are found is referred to as an electrons are found is referred to as an electron shellelectron shell..

There are rules as to the number of electrons that can be There are rules as to the number of electrons that can be held in each shell. held in each shell.

The arrangement of electrons within these shells is The arrangement of electrons within these shells is called the called the electron configurationelectron configuration..

The electrons that occupy the outermost shell are called The electrons that occupy the outermost shell are called valence electronsvalence electrons..

The chemical behaviour of an atom is a function of its The chemical behaviour of an atom is a function of its arrangement of electrons – in particular, the number of arrangement of electrons – in particular, the number of valence electrons in its outermost electron shell. valence electrons in its outermost electron shell.

Atoms are most stable when their outermost shell is full. Atoms are most stable when their outermost shell is full.

Making moleculesMaking molecules

Atoms are most stable when their Atoms are most stable when their outermost electron shell is full.outermost electron shell is full.

In order to achieve this state, atoms tend In order to achieve this state, atoms tend to combine with other atoms to form to combine with other atoms to form molecules.molecules.

There are two types of chemical bonds There are two types of chemical bonds that can hold the atoms within a molecule that can hold the atoms within a molecule together. These are together. These are ionic bondsionic bonds or or covalent bondscovalent bonds..

Ionic BondsIonic Bonds Atoms gain or loseAtoms gain or lose

electrons in order to electrons in order to increase stability.increase stability.

Atoms that lose electrons Atoms that lose electrons have a positive charge have a positive charge and are called and are called cationscations..

Atoms that gain electrons Atoms that gain electrons have a negative charge have a negative charge and are called and are called anionsanions..

An An ionic bondionic bond is an is an electrical attraction electrical attraction between two oppositely between two oppositely charged atoms or groups charged atoms or groups of atoms. of atoms.

Example of ionic bondingExample of ionic bondingNaCl or sodium chlorideNaCl or sodium chloride Sodium has 1 valence electron which it loses to become a cation Sodium has 1 valence electron which it loses to become a cation

with a charge of 1+with a charge of 1+ Chlorine has 7 valence electrons and acquires 1 extra electron from Chlorine has 7 valence electrons and acquires 1 extra electron from

sodium in order to become an anion with a charge of 1-sodium in order to become an anion with a charge of 1- The electrostatic attraction between positive sodium and negative The electrostatic attraction between positive sodium and negative

chloride (name changes when it forms an ion) holds the molecule chloride (name changes when it forms an ion) holds the molecule together.together.

Covalent BondsCovalent Bonds Atoms can share electrons Atoms can share electrons

in order to increase their in order to increase their stabilitystability

Covalent bonding is where Covalent bonding is where the atoms the atoms share pairsshare pairs of of outer shell or valence outer shell or valence electrons.electrons.

Covalent bonding may be Covalent bonding may be single or multiple, single or multiple, depending on the number depending on the number of pairs the atoms share. of pairs the atoms share.

Sometimes in covalent Sometimes in covalent bonds, one atom attracts bonds, one atom attracts the shared electrons more the shared electrons more strongly than the other, strongly than the other, resulting in a resulting in a polar polar covalentcovalent bond.bond.

Example of covalent bondingExample of covalent bonding

HH22O or waterO or water

Hydrogen (H) has 1 valence Hydrogen (H) has 1 valence electron but needs a total of 2 electron but needs a total of 2 in order to be a stable atom.in order to be a stable atom.

Oxygen has 6 valence Oxygen has 6 valence electrons but needs a total of 8 electrons but needs a total of 8 in order to be a stable atom.in order to be a stable atom.

By sharing electrons, each By sharing electrons, each hydrogen atom has two hydrogen atom has two valence electrons, thus filling valence electrons, thus filling their outer orbits. Likewise, their outer orbits. Likewise, oxygen now has 8 outer orbit oxygen now has 8 outer orbit electrons. electrons.

This makes for a good This makes for a good chemical bond and a stable chemical bond and a stable molecule.molecule.

Polar Covalent BondsPolar Covalent Bonds Polar covalent bonds are formed when one atom attracts Polar covalent bonds are formed when one atom attracts

the shared electrons more strongly than the other.the shared electrons more strongly than the other. Molecules that contain polar covalent bonds are referred Molecules that contain polar covalent bonds are referred

to as to as polar molecules polar molecules and molecules that are formed by and molecules that are formed by covalent bonds but don’t have polar bonds are called covalent bonds but don’t have polar bonds are called non-polar molecules.non-polar molecules.

The measure of the ability of an atom to attract electrons The measure of the ability of an atom to attract electrons in a bond is called in a bond is called electronegativityelectronegativity..

The region of the molecule which contains the atom with The region of the molecule which contains the atom with the greatest electronegativity will have a slightly negative the greatest electronegativity will have a slightly negative charge compared to the rest of the molecule. The rest of charge compared to the rest of the molecule. The rest of the molecule will have a slightly positive charge. This the molecule will have a slightly positive charge. This opposite charge separated by a distance is called a opposite charge separated by a distance is called a dipoledipole. .

Electronegativity Values (Pauling Scale)Electronegativity Values (Pauling Scale)

CC HH OO NN PP SS

2.52.5 2.12.1 3.43.4 3.03.0 2.22.2 2.62.6

ElectronegativityElectronegativity

The higher the value on the Pauling Electronegativity The higher the value on the Pauling Electronegativity Scale, the stronger the atom’s electron attracting power.Scale, the stronger the atom’s electron attracting power.

Simple analogy for electronegativitySimple analogy for electronegativity

Sharing electrons in Sharing electrons in covalent bonds is like covalent bonds is like trying to get a couple to trying to get a couple to share the doona equally.share the doona equally.

Someone is always going Someone is always going to have more pulling to have more pulling power!power!

One atom is always going One atom is always going to “hog” the electrons.to “hog” the electrons.

In a water molecule In a water molecule (H(H22O), the oxygen atom O), the oxygen atom will always attract the will always attract the shared electrons more shared electrons more than the hydrogen atoms than the hydrogen atoms do.do.

Interactions between molecules Interactions between molecules Intermolecular bonds are important in maintaining the 3D structure Intermolecular bonds are important in maintaining the 3D structure

of large biomolecules such as proteins and nucleic acids.of large biomolecules such as proteins and nucleic acids. These interactions also allow a molecule to bind specifically but These interactions also allow a molecule to bind specifically but

transiently with another molecule.transiently with another molecule. Individual interactions are weak and constantly break and reform at Individual interactions are weak and constantly break and reform at

the physiological temperatures of organisms.the physiological temperatures of organisms. Multiple interactions act together to produce highly stable and Multiple interactions act together to produce highly stable and

specific associations between parts of a large biomolecule and/or specific associations between parts of a large biomolecule and/or between different molecules.between different molecules.

Four types of interactions are responsible for intermolecular bonds:Four types of interactions are responsible for intermolecular bonds: Hydrogen bondsHydrogen bonds Van der Waals interactions (transient dipoles)Van der Waals interactions (transient dipoles) Hydrophobic bondsHydrophobic bonds Ionic interactionsIonic interactions

Hydrogen bondsHydrogen bonds(dipole-dipole bonding)(dipole-dipole bonding)

Weak electrostatic Weak electrostatic attraction between the attraction between the negative region (negative region (δδ-) of -) of one polar molecule one polar molecule and the positive and the positive region (region (δδ+) of another +) of another polar molecule.polar molecule.

Van der Waals interactions Van der Waals interactions (transient dipoles)(transient dipoles)

At very short distances all At very short distances all atoms and molecules show atoms and molecules show a weak bonding interaction a weak bonding interaction due to their fluctuating due to their fluctuating electrical charges.electrical charges.

Electrical charges fluctuate Electrical charges fluctuate due to the uneven due to the uneven distribution of electrons as distribution of electrons as they orbit the nucleus of an they orbit the nucleus of an atom. The larger the atoms atom. The larger the atoms involved the greater the involved the greater the fluctuation in charge.fluctuation in charge.

Hydrophobic bondsHydrophobic bonds Non-polar molecules Non-polar molecules

such as fats or oils will such as fats or oils will aggregate together when aggregate together when placed in a polar placed in a polar substance such as water. substance such as water. This aggregation is This aggregation is referred to as a referred to as a hydrophobic bonds. hydrophobic bonds.

It is not a separate It is not a separate bonding force but is due bonding force but is due to water molecules to water molecules excluding the non-polar excluding the non-polar molecules, forcing them molecules, forcing them to adhere to one another.to adhere to one another.

Red molecules are H2O

Ionic interactionsIonic interactions

Ionic compounds are generally soluble in water due to Ionic compounds are generally soluble in water due to ionic interactions with water molecules. ionic interactions with water molecules.

Atoms in functional groups can donate or accept protons Atoms in functional groups can donate or accept protons (H+) forming ions that interact with other charged groups (H+) forming ions that interact with other charged groups on atoms on different molecules.on atoms on different molecules.

Molecule with NH2 group attached has gained H+ so becomes positive ion.

Molecule with COOH group attached has lost H+ so becomes negative ion.

Inorganic and Organic MoleculesInorganic and Organic Molecules

Both living and non-living things are made from Both living and non-living things are made from the same chemical elements but their is a the same chemical elements but their is a difference in the way that these elements are put difference in the way that these elements are put together to make larger molecules.together to make larger molecules.

Organic compoundsOrganic compounds contain carbon and contain carbon and hydrogen (and sometimes other elements such hydrogen (and sometimes other elements such as oxygen and nitrogen). They are called as oxygen and nitrogen). They are called organic compounds as the first ones studied organic compounds as the first ones studied were produced by or found in living organisms.were produced by or found in living organisms.

All other compounds are called All other compounds are called inorganic inorganic compoundscompounds..

Biologically ImportantBiologically ImportantInorganic MoleculesInorganic Molecules

Inorganic molecules important for living organisms include:Inorganic molecules important for living organisms include: nitrogennitrogen – present in all proteins and nucleic acids. Fixed from the – present in all proteins and nucleic acids. Fixed from the

atmosphere by nitrogen-fixing bacteriaatmosphere by nitrogen-fixing bacteria mineralsminerals – found in the cytosol and structural components of cells and – found in the cytosol and structural components of cells and

in the molecules of enzymes and vitamins. Important minerals include in the molecules of enzymes and vitamins. Important minerals include phosphorous, potassium, calcium, magnesium, iron, sodium, iodine and phosphorous, potassium, calcium, magnesium, iron, sodium, iodine and sulfur.sulfur. Examples: phosphorous present in phospholipids of cell Examples: phosphorous present in phospholipids of cell membrane and in ATP, magnesium important component of chlorophyll, membrane and in ATP, magnesium important component of chlorophyll, iron an important component of haemoglobiniron an important component of haemoglobin

oxygenoxygen – most cells require oxygen to release usable energy from food – most cells require oxygen to release usable energy from food moleculesmolecules

carbon dioxidecarbon dioxide – main source of carbon for the production of organic – main source of carbon for the production of organic molecules despite the fact that it only makes up 0.035% of atmosphere molecules despite the fact that it only makes up 0.035% of atmosphere by volume. Organic molecules (sugars) are eaten by animals and by volume. Organic molecules (sugars) are eaten by animals and carbon dioxide released back into atmosphere as an end-product of carbon dioxide released back into atmosphere as an end-product of cellular respiration.cellular respiration.

waterwater - chemical reactions in cells occur in a water environment - chemical reactions in cells occur in a water environment

More about carbonMore about carbon All the chemicals of life on this planet, with the exception of water, are based on the All the chemicals of life on this planet, with the exception of water, are based on the

carbon atom.carbon atom. It is the valency of carbon that allows it to form the base of all chemicals of life. The It is the valency of carbon that allows it to form the base of all chemicals of life. The

carbon atom has four valence electrons, meaning it can form four stable covalent carbon atom has four valence electrons, meaning it can form four stable covalent bonds with other atoms. bonds with other atoms.

Carbon atoms can also bond with other carbon atoms to form straight and branched Carbon atoms can also bond with other carbon atoms to form straight and branched chain and ring structures of various sizes and complexity that form the backbone to chain and ring structures of various sizes and complexity that form the backbone to many biological molecules. many biological molecules.

Carbon atoms can share more than one pair of electrons between two carbon atoms, Carbon atoms can share more than one pair of electrons between two carbon atoms, resulting in the formation of double and triple bonds. resulting in the formation of double and triple bonds.

Molecules containing only carbon and hydrogen atoms are known as hydrocarbons. Molecules containing only carbon and hydrogen atoms are known as hydrocarbons. Hydrocarbons are non-polar and hence insoluble in water.Hydrocarbons are non-polar and hence insoluble in water.

What creates the diversity and chemical properties of carbon based molecules is the What creates the diversity and chemical properties of carbon based molecules is the addition of other groups of atoms to the hydrocarbon backbone. addition of other groups of atoms to the hydrocarbon backbone.

Groups of atoms that confer water solubility and chemical properties to the Groups of atoms that confer water solubility and chemical properties to the hydrocarbon chain are known as functional groups. hydrocarbon chain are known as functional groups.

These groups of atoms are more reactive than the hydrocarbon portion of These groups of atoms are more reactive than the hydrocarbon portion of biomolecules and often contain highly electronegative atoms which convey a polarity biomolecules and often contain highly electronegative atoms which convey a polarity to their end of the molecule while the hydrocarbon chain is non-polar.to their end of the molecule while the hydrocarbon chain is non-polar.

WaterWater Water covers about 75% of our planet’s surface and Water covers about 75% of our planet’s surface and

makes up 70% to 90% of the cell content of living things. makes up 70% to 90% of the cell content of living things. It has a number of It has a number of unique propertiesunique properties that support life that support life

on Earth. on Earth. These properties are a direct result of the polar nature of These properties are a direct result of the polar nature of

the water moleculethe water molecule

Why is water so special?Why is water so special?PROPERTY OF WATERPROPERTY OF WATER EXPLANATION OF PROPERTYEXPLANATION OF PROPERTY

CohesionCohesion Liquid water is cohesive due to the constant forming and Liquid water is cohesive due to the constant forming and reforming of hydrogen bonds that hold the molecules reforming of hydrogen bonds that hold the molecules together.together.

High specific heatHigh specific heat Heat must be absorbed to break hydrogen bonds before Heat must be absorbed to break hydrogen bonds before the water molecules can move faster and the the water molecules can move faster and the temperature rises. temperature rises.

This means cell does not overheat despite the heat This means cell does not overheat despite the heat energy produced by many reactions happening within the energy produced by many reactions happening within the cell.cell.

Heat of vaporisationHeat of vaporisation A large amount of heat is required to break the hydrogen A large amount of heat is required to break the hydrogen bonds for liquid water to be converted to water vapour.bonds for liquid water to be converted to water vapour.

Solid is less dense than liquidSolid is less dense than liquid Hydrogen bonding creates a crystalline lattice in which Hydrogen bonding creates a crystalline lattice in which the water molecules are spaced further apart, reducing the water molecules are spaced further apart, reducing the density of the solid.the density of the solid.

SolventSolvent Water molecules are attracted to solutes that carry a Water molecules are attracted to solutes that carry a charge. The solute is said to have dissolved into charge. The solute is said to have dissolved into solution.solution.

Both polar molecules and ionic compounds are easily Both polar molecules and ionic compounds are easily dissolved in water.dissolved in water.

Water as a pH bufferWater as a pH buffer pH is a measure of the hydrogen pH is a measure of the hydrogen

ions in a solution and hence the ions in a solution and hence the state of acidity or alkalinity of a state of acidity or alkalinity of a solution.solution.

pH scale is 0 to 14.pH scale is 0 to 14. Less than 7 indicates higher Less than 7 indicates higher

concentration of Hconcentration of H+ + (acidic (acidic solution)solution)

Greater than 7 indicates higher Greater than 7 indicates higher concentration of OHconcentration of OH-- (alkaline (alkaline solution)solution)

Pure water has pH of 7.0 and is a Pure water has pH of 7.0 and is a neutral solution but water readily neutral solution but water readily ionizes or break ups to form Hionizes or break ups to form H+ +

and OHand OH- - ions. ions. This allows the cellular fluids to This allows the cellular fluids to

balance changes in pH as binding balance changes in pH as binding of these ions to other substances of these ions to other substances within the cell prevents severe within the cell prevents severe changes in the pH of a cell or fluid.changes in the pH of a cell or fluid.

I’m a little water molecule!!!I’m a little water molecule!!!(to the tune of “I’m a little teapot”)(to the tune of “I’m a little teapot”)

I’m a little I’m a little water moleculewater molecule

They call me They call me HH22OO

I’m not to good at sharingI’m not to good at sharingMy My H more positiveH more positive than my O than my OThat’s why they call meThat’s why they call me polar polarCause my Cause my molecules attract each othermolecules attract each otherIn between them, H bondsIn between them, H bondsI’m a BIG SELF LOVER!I’m a BIG SELF LOVER!