Bio 111: Molecules of life

Question 1

Different types of energy (kinetic)

Answer 1

Kinetic - Energy associated with movement. Moving objects can perform work by imparting motion onto something. Thermal is also kinetic energy- Random movement of atoms or molecules.

Question 2

Different types of energy (potential)

Answer 2

Potential energy is the energy that matter possesses because of its location or structure. Chemical energy is also potential energy because the molecule can release energy by taking part in chemical reactions.

Question 3

Elements

Answer 3

Matter is made up of elements. An element is a substance which cannot be broken down to another substance by chemical reactions. 25 of the naturally occurring elements are essential for life.

Question 4

Atom

Answer 4

Smallest unit of matter which still retains the properties of that element. Atoms are made of protons and neutrons. Protons, positively charged and neutrons, neutral and are both located in the nucleus. Electrons, negatively charged- form a cloud around the nucleus.

Question 5

Mass of subatomic particles

Answer 5

Each proton or neutron has a mass of 1.7x10^-24g. This is rather small unit of mass, therefore, we use a unit of measurement called the DALTON. Protons and neurons both weigh 1 Dalton. 1 Dalton= 1 atomic mass unit. Mass of electron is equal to 1/2000th of the mass of a neutron or a proton. The charges of the electron and proton are equal and opposite. The number of protons is equal to the number of electrons in a neutral atom.

Question 6

Atomic number

Answer 6

Refers to the number of protons in the nucleus and is distinct for each atom. In transcript atomic number is written on bottom left hand side of atom.

Question 7

Atomic Mass

Answer 7

= Total number of protons, neutrons and electrons. Generally, except in very accurate work, the contribution of the mas of the electron is negligible.

Question 8

Isotopes

Answer 8

Elements can exist with different number of neutrons but the same number of protons. The element remains the same and behave the same in chemical reactions. Carbon exists as 3 different isotopes; carbon 12/13/14.

Question 9

Atomic Orbitals

Answer 9

Not all of the electrons in an atom are equivalent. The electrons occupy orbitals of different energies. The S orbitals are spherical and P orbitals are dumbbell shaped. Only 2 electrons occupy each orbital and they are occupied in order of lowest energy first, then next highest energy and so on.
Filled orbitals are more stable than filled. One more electron or one less electron are both very reactive, as they try to lose or gain an electron respectively. When 2 atoms approach each other during a chemical reaction, the electrons in the outermost orbitals interact to create bonding. By reacting together, atoms form compounds which have different properties to the component elements.

Question 10

Covalent bonds

Answer 10

Sharing of a valence electrons by two atoms. Can be non-polar bonds where there is equal sharing of electrons within the covalent bond or polar, where there is unequal sharing of electrons within the covalent bond. Polar covalent bonds arise because the two elements being joined have different electronegativities. In a polar covalent bond, the electrons in the covalent bond will be pulled more towards the electronegative atom than the other atom and because electrons have a negative charge, this will impart a slightly negative charge upon the electronegative atom.

Question 11

Hydrogen Bonds

Answer 11

These are weak intermolecular forces and form with a Hydrogen atom, covalently attached to an electronegative atom, is also attracted to another electronegative
atom. FON

Question 12

Ionic Bonds

Answer 12

Sometimes the two atoms which come together are very different in their attraction for valence electrons. One atom may be very electronegative and the other may be very electropositive. e.g Na and Cl. In this example the electronegative atom strips away an electron from the partner. This results in one positively charged ion and one negatively charged ion. The attractive force between the ions is called an ionic bond. Cation- Positive ion. Anion- Negative ion.

Question 13

Van der waals

Answer 13

Molecules bonded by non-polar covalent bonds can stick together by virtue of weak interactions. The electrons in a molecule are constantly moving and not always symmetrically placed. Therefore, you may happen to get a positive and a negative charge in one particular region of a molecule, quite by chance which can then interact with the opposite charge on an adjacent molecule. This molecules have to be close to interact this way.

Question 14

Bonding in water (orbitals description)

Answer 14

Oxygen has an atomic number of 8 and therefore has 8 electrons. The first orbital to get filled is 1s, then 2s, then 2p (3 of those), therefore we can write oxygens electron configuration as 1s2 2s2 2p4. 3 P orbitals are at right angles to one another. P orbitals can have a maximum of 6 electrons, oxygen only has 4 in the p orbitals, therefore for electron to become stable it needs 2 more electrons. To gain these two electrons oxygen can share 2 electrons for 2 hydrogen atoms. This covalent bond also provides hydrogen with a 1s2 orbital, achieving stability for all 3 atoms.

Question 15

Hydrogen bonding in water

Answer 15

Two ends of water molecules have opposite charges- we call this kind of molecule a polar molecule. The oxygen has a partial negative charge and the hydrogen atoms have a partial positive charge. This is because oxygen is more electronegative than hydrogen.
The polar nature of water means that they can attract and bind weakly to one another via hydrogen bonds. Hydrogen bonds are weak bonds (10-20KJ/mole) but collectively are strong.

Question 16

high surface tension and Cohesion

Answer 16

Water molecules binding to one another enable water to have a high surface tension, which means that some insects can walk on the surface of the water.
Water has a fairly low molecular mass, thus you would expect it to be a gas at room temperature. Water is a liquid at room temperature because the water molecules are joined together via hydrogen bonding. In order to get water into the gaseous phase, energy needs to be supplied to break the hydrogen bonds apart.

Question 17

Heat of vaporisation

Answer 17

Energy which must be supplied to 1g of a material in order for the molecules to move from a liquid to a gas phase.

Question 18

High specific heat capacity

Answer 18

Amount of energy which must be absorbed to raise the temperature of 1g of that substance by 1C
A calorie is the amount of heat which 1g of water releases when it cools by 1C. (1 calorie= 4.184 joules; 1 joule=0.239.

Question 19

Insulation in water

Answer 19

Ice is less dense than water. This is a result of each molecule being bonded to four neighbouring water molecules to give a crystal lattice. As ice melts, some of the hydrogen bonds break, enabling the water molecules to slip closer to one another. Ice is about 10% less dense than water at 4C , which means that ice floats on water. This insulates the water beneath essential for the survival of life in deep water.

Question 20

Water acts as a solvent

Answer 20

Many solutes dissolve in aqueous solutions, e.g sodium chloride. when sodium and chloride ions are exposed to water. The hydrogens in water will bind to the negatively charged chloride ions, eventually surrounding each chloride ion in its own hydration shell and thereby removing it from the sodium chloride crystal lattice. The oxygen s will similarly bind to the sodium ions, eventually giving sodium ion its own hydration shell and removing it from the sodium chloride crystal lattice. Eventually the salt dissolves to give an aqueous solution of sodium chloride.

Question 21

Moles and molarity

Answer 21

Molecular Mass is the sum of masses of all atoms in a molecule (in Daltons).
1 Mole of a substance will always contain 6.02x10^23 molecules (Avogadro’s number)
There are 6.02x10^23 Daltons in 1g, so the molecular weight of any compound in grams contains 6.02x10^23 molecules.
This has the advantage that if you take the molecular mass of any compound in grams, it will contain exactly the same number of molecules.

Question 22

Concentration is given in terms of molarity of a solution

Answer 22

A 1 molar solution of compound X contains he molecular mass in grams in a total of 1L of solution (1mole/L or 1mole/dm^3). E.g Sodium hydroxide solution- relative molecular mass= 40. Take 40g of NaOH and dissolve water then bring the total volume up to 1L of solution with water, then you have made a 1 Molar solution.

Question 23

Water dissociation constant

Answer 23

Dissociation of water is a reversible reaction which eventually reaches an equilibrium where the rate of the backward reaction equals the rate of the forward reaction. This is called the K’w to make it distinct from kw. But because water molecules do not dissociate in pure water, the equilibrium lies heavily to the left. In pure water only 1 molecule in 554000000 is dissociated. The concentration in pure water is 55.6 and is constant and therefore the equilibrium constant is expressed like this: Kw= [H+][OH-].
Concentration of each ion in pure water is 10^-7M , therefore we can deduce that Kw at room temperature and pressure is 10^-14

Kw differs from K’w.

Question 24

pH

Answer 24

Kw in water stays constant at 10^-14.
If you add acid the [H+] increases and the [OH_] decreases so that Kw remains constant at 10^-14 and vice versa.
e.g. 0.1M HCl has 10^-1 [H+] and therefore, [OH] is 10^-13.
We define pH of a solution as -log[H+].

Question 25

Common functional groups

Answer 25

OH= Alcohol or hydroxyl
NH2= amine
SH= sulfhydryl, common in proteins. The amino acid which contains thiol group is cysteine. The important thing about cysteine amino acids is that when oxidised, they can dimerise thus linking two parts of the protein chain. 
CHO (end of chain)= Aldehyde
COC= Ketone
CONH2= Amide
COOH= Carboxylic acids. At pH 7 carboxylic acids dissociate to give H+ and a carboxylate group.
PO4= Phosphate group

Question 26

Isomers

Answer 26

Have the same number of atoms of the same elements but the compounds are joined together in different ways, giving them properties
STRUCTURAL isomers differ in covalent partners
GEOMETRIC isomers different in the arrangement around a double bond. If they are on the same side of the double bond it is Cis if they are on opposite sides they are trans-isomers.

Question 27

Enantiomers

Answer 27

The molecules differ in only the spatial arrangement of groups around a central asymmetric or chiral carbon. The 4 groups around the carbon atom need to be different. Two enantiomers are mirror images of one another and they cannot be superimposed upon one another. The compounds have identical chemical and physical properties and therefore it is notoriously difficult to separate them. The way in which they differ is that they happen to rotate plane polarised light in opposite directions.