Chapter 2: Important Molecules And Their Properties Flashcards by Hannah Emery

Which 6 elements do most biological molecules consist of? (EXTRA: name 3 other common biological elements)

Hydrogen
Carbon
Nitrogen
Oxygen
Phosphorus
Sulphur

EXTRA:
Helium, Neon, Argon

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What are the atomic numbers of hydrogen, carbon, nitrogen, oxygen, phosphorus, an sulphur?

Hydrogen: 1
Carbon: 6
Nitrogen: 7
Oxygen: 8
Phosphorus: 15
Sulphur: 16

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What are the atomic weights of hydrogen, carbon, nitrogen, oxygen, phosphorus, an sulphur?

Hydrogen: 1
Carbon: 12
Nitrogen: 14
Oxygen: 16
Phosphorus: 31
Sulphur: 32

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Define molecular weight

The weight of a molecule, obtained by adding up the weight of the individual atoms (the value is equal to the weight of Nₐ molecules).

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What is the value of Avogadro’s number (Nₐ)?

Nₐ = 6.02 x 10^23 molecules (particles) per mole
Units: /mol

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What is a covalent bond?

A bond in which two participating atoms share electrons to complete their shells.

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What is an ionic bond?

A bond in which one atom transfers an electron to another to form a molecule

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Define chemical group

A small molecular subunit consisting of a few atoms which can be found in a similar configuration on a variety of different molecules.

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How many electrons do carbon, nitrogen, oxygen, and hydrogen require to form a stable covalent bond?

Carbon: 4
Nitrogen: 3
Oxygen: 2
Hydrogen: 1

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Describe the hydroxy-group

An oxygen, and hydrogen joined with a covalent bond. This is a non-stable group as the dissociation of oxygen and hydrogen can take place.

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Describe the acid-group

Two oxygen, a carbon, and a hydrogen atom joined with several covalent bonds. This is a non-stable group as the dissociation of hydrogen from the acid group can take place, resulting in a chemical group that carries one elementary unit of charge (the charge of one electron). Hence, this group can be a carrier of charge.

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Describe the amino-group

A nitrogen, and two hydrogen atoms joined with multiple covalent bonds, also known as a carboxyl group. The nitrogen bond also forms another covalent bond with a separate carbon atom when forming and amino acid. Association can take place for this group by gaining hydrogen nuclei (protons) which allows it to become a positively charged amino-group.

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Describe the structure of an amino acid

The combination of an amino-group, acid-group, hydrogen and an R-group (of which there are ~22 for amino acids) joined together with covalent bonds. Amino acids bond together via peptide bonds to produce a protein.

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What is an aromatic ring?

A ring of six carbons joined by three double bonds (where atoms are share four electrons, two from each atom, rather than two).

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Describe the methyl-group

A carbon and three hydrogen atoms bonded.

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Double-bonded carbons ______ bond in a chain longer than two carbon atoms (e.g. C=C=C=C).

Cannot

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What is the length of 1Å (1 Ångstrom) in metres?

1Å = 10^-10 m

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What is the mass of 1 Dalton in kg?

1 Da = 1.661 x 10^-27 kg = 1 u (unified atomic mass unit)

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The unified atomic mass unit, with units of Daltons, are equivalent to the weight of _ ________ ____.

1 hydrogen atom

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What are the two most important properties of water?

Electric dipole moment and dielectric constant

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Define electric dipole moment

A measure of the overall polarity of a system, represented by a vector pointing from the negative to positive charge.

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What is the equation for the magnitude of the electric dipole moment?

µ = electric dipole moment
q = charge
r = separation distance

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What is the electric dipole moment of water at 27ºC? (EXTRA: what is the charge and separation distance for the electric dipole moment at these temperatures?)

2.95 D

EXTRA: q = 0.7e (1.121 x 10^-19 C), r = 8.8 x 10^-11 m

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What is the value of 1 Debye in Cm (coulomb metres)?

1 D = 3.34 x 10^-30 Cm

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Water is a dipole since the electron density in water is ___ _______. This means the ______ ___________ can be approximated as two separate charges, __, separated by a distance, __.

Not uniform Charge distribution ±q r

What is the name for the bond between water molecules?

Hydrogen bonds

What is the bond energy of a hydrogen bond?

U = 0.03 x 10^-18 J

How many hydrogen bonds can form from one molecule of water?

Four

Define dielectric constant (also known as relative permittivity)

A ratio of the permittivity of the water to the permittivity of a vacuum (8.854 x 10^-12 C^2N^-1m^-2).

What is the dielectric constant of water at 25ºC?

~80

Give the Coulomb equation for the potential energy of two charges in water

U = potential energy q = charge ε = permittivity ε_0 = permittivity of a vacuum ε_r = relative permittivity r = separation distance

If an electric field is applied to a molecule, it can be distorted and its ________ _______ ______ ______ will align with it as an ______ ______ ______ is generated.

Permanent electric dipole moment Induced dipole moment

Give the equation for an induced dipole moment

µ* = induced dipole moment α = polarisability E = electric field strength

Define induced dipole moment

A dipole moment that is created by a molecule coming into contact with an electric field/ polar molecule.

Give the equation for polarisability volume in terms of polarisability (EXTRA: give units for polarisability volume)

α’ = polarisability volume ε_0 = permittivity of a vacuum EXTRA: units: m^2

What is the purpose of the Debye equation?

To link the relative permittivity of a medium and the electric dipole moment of its molecules. It is only an approximation for water due to its dynamic nature.

Give the Debye equation

ρ = density k_b = Boltzmann’s constant M = molar weight (= 18 g/mol.) T = temperature

How is the refractive index of water related to the permittivity of water?

n_r = refractive index of water ε_r = permittivity of water

What are the three types of molecules that the medium of water is made up of?

H2O OH⁻ ⁺H3O

Why is water made up of multiple types of molecules?

Because H2O can dissociate into a hydrogen ion (H⁺) and a hydroxyl ion (OH⁻) which both carry charge and can can interact to form the 3 types of molecules.

What is the dissociation rate of water?

r_D = 2.5 x 10^-5 /s

What is the molar concentration of water?

1000g / 18g/mol. = 55.6 mol/L Mass of 1L of water / molar weight

Define pH value

A measure of how acidic or alkaline a solution is, found using the amount of free hydrogen and hydroxyl ions in the aqueous solution.

Give the equation for the pH value of water

[ ] = molar concentration of positively charged complex

Give the equation for the dissociation constant of water

K_D = dissociation constant

Derive the equation for pH using the equation for the dissociation constant of water

Give the equation for pH in terms of pK

Define pK value

The negative log value of the dissociation constant, often used to determine the strength of an acid.

If the acceptor concentration equals the donor concentration for a substance, the pH value ____ ______ the pK value.

Will equal

Define Gibbs free energy

The change in free energy for a process, calculated by measuring the difference between the change in enthalpy and the product of temperature and change in entropy.

Give the equation for Gibbs free energy

∆G = change in Gibbs free energy ∆H = change in enthalpy T = temperature ∆S = change in entropy

Define enthalpy

A thermodynamic quantity equal to the total heat content of a system, hence, equal to the sum of the internal energy of the system and the product of pressure and volume.

Define entropy

A thermodynamic quantity that measures how much of a systems thermal energy per unit temperature is unavailable for doing useful (mechanical) work, often referred to as a systems degree of disorder.

Give the equation that relates the dissociation constant to the change in Gibbs free energy per mole

∆Gº = change in Gibbs free energy per mole R = ideal gas constant

Define amino acid

A simple organic compound containing both an acid and an amino functional group. 20 amino acids appear in the genetic code and comprise proteins.

Acid groups, which have the structure R-COOH, can dissociate into ______ and __.

R-COO⁻ H⁺

What is the dissociation constant equation for an acid group?

Give the Henderson-Hasselbalch equation (EXTRA: give the Henderson-Hasselbalch equation for an acid group)

For the amino group of an amino acid, the H acceptor is ___ and the H donor is ____

NH2 NH3⁺

Define nucleotide

The units that make up the macromolecules DNA and RNA. They consist of a nitrogenous base (either adenine, guanine, cytosine, uracil, or thymine), a pentose sugar (either ribose or deoxyribose), and a phosphate.

What are the two purines?

Adenine Guanine

What are the three pyrimidines?

Cytosine Uracil Thymine

When forming a DNA double helix, purines will always pair with __________.

Pyrimidines

What are the base pair combinations for DNA?

A-T T-A C-G G-C

What are the base pair combinations for RNA?

A-U T-A C-G G-C