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Chapter 2

BIO206H5 Chapter Notes - Chapter 2: Covalent Bond, Non-Covalent Interactions, Electron Shell

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George S Espie

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Chapter 2: Chemical Components of Cells
Chemical Bonds
The chemistry of life is based mostly on carbon compounds, which is the study of Organic Chemistry
Second, it depends on chemical reactions that take place in watery, or aqueous solutions and in the narrow range of temperatures on
Third, it is very complex. Even the simplest cell is complicated in its chemistry
Fourth, it is dominated and coordinated by a collection of polymeric molecules, whose properties allow the cell and the organism to grow
and reproduce
Polymeric Molecules: chains of chemical subunits that are linked end-to-end
Fifth, the chemistry of life is tightly regulated
Matter is made up of a combination of elements
Cells Are Made of Relatively Few Types of Atoms
Each atom has a positively charged nucleus, which is surrounded by a cloud of negatively charged electrons.
The electrons are held there by electrostatic attraction to the nucleus
The Nucleus contains two types of subatomic particles: protons and neutrons
Number of protons in an atom's nucleus determines its Atomic Number
Electrical charge of each proton is equal and opposite to the charge that is carried by a single electron
Because the atom is neutral, the number of negatively charged electrons that surround the nucleus is equal to the number of positively
charged protons in the nucleus
Neutrons have the same mass as protons
They contribute to the stability of the nucleus. If there are too many or too few, the nucleus may disintegrate by radioactive decay
Elements that can exist in several physically different but chemically identical forms are called Isotopes.
Atomic Weight (Molecular Weight): mass relative to that of a hydrogen atom
It is equal to the number of protons + neutrons that an atom or molecule contain
Because the electrons are really light, they don't contribute to the total mass
Mass of an atom or molecule is measured in Dalton
Avagadro's Number allows us to relate everyday quantities of chemicals to numbers of individual atoms or molecules
Living organisms are only made up of a few elements, a few of which are: Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O)
The Outermost Electrons Determine How Atoms Interact
Protons and neutrons are welded together tightly in an atoms nucleus
In living tissues, only the electrons of an atom go through rearrangement
They form the accessible part of the atom and specify the rules of chemistry by which atoms combine to form molecules
Electrons are in continuous motion around the nucleus, but these motions obey different laws
These laws say that electrons in an atom can exist only in certain regions of movement
There is also a limit to the numbers of electrons that can be accommodated in an orbit of a given type (electron shell)
Electrons closest to the positive nucleus are attracted more strongly and it occupies the inner, most tightly bound shell
Inner shell can hold 2 electrons
Second and third shell can hold 8 electrons
Fourth and Fifth shell can hold 18 electrons each
The arrangement of electrons is the most stable when all of the electrons are in the most tightly bound state
Atoms found in living organisms all have their outermost shells incompletely filled, and so they are able to react with one another to
form molecules
Incompletely filled electron shells are less stable than one that is filled before it, so the atoms with incomplete outer shells have a
strong tendency to interact with other atoms to gain or lose electrons to get a completed outermost shell
Electron exchange can happen by transferring electrons from one atom to another, or by sharing electrons between two atoms
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Ionic Bond: formed when electrons are donated by one atom to another
Covalent Bond: formed when two atoms share a pair of electrons
The number of electrons an atom must gain or lose to get a filled outer shell determines the number of bonds that the atom can make
The state of the outer electron shell determines the chemical properties of an element
Covalent Bonds Form by the Sharing of Electrons
All characteristics of a cell depend o the molecules it contains
Molecule: cluster of atoms that are held together by a covalent bond
The shared electrons form a cloud of negative charge that is densest between the two positively charged nuclei
This electron density helps to hold the nuclei together by opposing the repulsion between their positive charges
The attractive and repulsive forces are in balance when the nuclei are separated by a certain distance. This is called Bond Length
When one atom forms covalent bonds with several others, these multiple bonds have definite orientations in space relative to one
Covalent bonds between multiple atoms have specific bond angles, as well as specific bond lengths and bond energies
There Are Different Types of Covalent Bonds
Most covalent bonds involve sharing of two electrons. These are called Single Bonds
Some covalent bonds involve sharing of more than one pair of electrons
When four electrons are shared, it forms two bonds, also called Double Bond
Double bonds are shorter and stronger than single bonds, and they also have an effect on the three-dimensional geometry of
molecules that contain them
A single covalent bond allows the rotation of one part of the molecule relative to the other along the bond axis.
A double bond prevents this rotation, which produces a more rigid and less flexible arrangement of atoms
Some molecules contain atoms that share electrons in a way that produces bonds that are intermediate in character between single
and double bonds (Benzene)
When atoms joined together in a single bond belong to different elements, the two atoms attract the shared electrons in different
Polar Covalent Bond: covalent bonds in which the electrons are shared unequally
Polar Structure: one in which the positive charge is concentrated towards one end of the molecule (positive pole), and the negative
charge is concentrated towards the other end (negative pole)
Covalent Bonds Vary in Strength
Bond Strength is measured by the amount of energy that must be applied to break the bond
Expressed in kcal/mol OR kJ/mol
Kilocalorie is the amount of energy needed to raise the temperature of 1 litre of water by 1°C
1 kcal = 4.2 kJ
typical covalent bonds are stronger than these thermal energies , so they resist to be pulled apart by thermal motion
When water is present, covalent bonds are much stronger than ionic bonds
In ionic bonds, the electrons are transferred rather than shared
Ionic Bonds Form by the Gain and Loss of Electrons
When an electron jumps from one atom to another atom, both atoms become electrically charged ions
The atom that lost the electron now has one less electron than it has protons in its nucleus. It therefore has a net single positive charge.
The atom that gained the electron now has one more electron than it has protons in its nucleus. It therefore has a net single negative
Because of their opposite charges, the ions are attracted to each other and are held together by an ionic bond
Ions that are held together by an ionic bond are generally called Salts rather than molecules
Because of the interaction between ions and water molecules, many salts are highly soluble in water
They dissociate into individual ions, and each ion gets surrounded by a group of water molecules
Positive ions are called Cations
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Negative Ions are called Anions
Noncovalent Bonds Help Bring Molecules Together in Cells
In aqueous solutions, ionic bonds are 10-100 times weaker than the covalent bonds that hold atoms together
Most of biology depends on specific but transient interactions between one molecule and another
Even though non-covalent bonds are quite weak, their energies can sum to create an effective force between two molecules
Ionic bonds that hold together the Na and Cl ions in a salt crystal are a form of Noncovalent bond called Electrostatic Attraction
Electrostatic Attractions are strongest when the atoms involved are fully charged
But a weaker electrostatic attraction also occurs between molecules that contain polar covalent bonds
Polar covalent bonds are very important in biology because they allow molecules to interact through electrical forces
When present in large numbers, weak non-covalent bonds on the surface of large molecules can promote strong and specific binding
Hydrogen Bonds are Important Noncovalent Bonds For Many Biological Molecules
Water makes up 70% of the bodies weight
In each H2O molecule, two atoms are linked to the O by a covalent bond
it is highly polar because the O is highly attractive for electrons, and the H is weakly attractive
Because of this, there is an unequal distribution of electrons in a water molecule
When a positively charged region of one water molecule comes close into contact with a negatively charged region of a second water
molecule, the electrical attraction between them can create a weak bond called a Hydrogen Bond
Hydrogen bonds are more weaker than covalent bonds and they are easily broken by random thermal motions
Each water molecule can from hydrogen bonds with two other water molecules. This produces a network in which hydrogen bonds are
continuously being formed and broken
Because of these interlocking hydrogen bonds, water at room temperature is a liquid that has a high boiling point and a high surface
Without hydrogen bonds, life would not exist
A hydrogen bond can form whenever a positively charged H atom that is linked to a molecule by polar covalent linkage comes into
close contact with a negatively charged O, N, or F on another molecule
Hydrogen bonds can also form between different parts of the same molecule. This helps hold the molecule in a particular shape
Hydrocarbons are important hydrophobic cell constituents
In a hydrocarbon, the H atoms are covalently linked to a C atom by nonpolar bonds
Because lipids do not dissolve in water, they can form the thin membranes barriers that keep aqueous interior of the cell separate from
the aqueous exterior of the cell
Some Polar Molecules Form Acids and Bases in Water
Important reaction in cell is one where a molecule that has a high polar covalent bond between a H and another atom dissolves in
The H atom gives up its electron almost entirely to the other atom, so it exists as a positively charged H nucleus (H+)
When water molecules surround this polar molecule, the proton will be attracted to the partial negative charge on the Oxygen atom on
the water molecule. This will create a H3O+
Substances that dissolve in water and form H3O+ are called Acids
The higher the concentration of hydronium ions, the more acidic the solution is
Acids can either be strong or weak, depending on how readily they give up their protons to water
Strong acids (like HCl) lose their protons easily
Acetic Acid is a weak acid because it holds on to its proton much tighter when dissolved in water
Because protons can be passed readily to many types of molecules in cells, the H+ concentration inside of the cell needs to be
Acids (especially weak acids) give up their protons more readily if the hydronium concentration is low and will accept them more
readily if the hydronium concentration is high
Bases accept a proton when dissolved in water
Bases raises the concentration of OH ions by removing a proton from a water molecule
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