Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

PHYS3012: Molecular BioPhysics > Chapter 2: Important Molecules And Their Properties > Flashcards

Chapter 2: Important Molecules And Their Properties Flashcards

1
Q

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

A
  • Hydrogen
  • Carbon
  • Nitrogen
  • Oxygen
  • Phosphorus
  • Sulphur

EXTRA:
Helium, Neon, Argon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

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

A
  • Hydrogen: 1
  • Carbon: 6
  • Nitrogen: 7
  • Oxygen: 8
  • Phosphorus: 15
  • Sulphur: 16
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

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

A
  • Hydrogen: 1
  • Carbon: 12
  • Nitrogen: 14
  • Oxygen: 16
  • Phosphorus: 31
  • Sulphur: 32
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Define molecular weight

A

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).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

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

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is a covalent bond?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is an ionic bond?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Define chemical group

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

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

A
  • Carbon: 4
  • Nitrogen: 3
  • Oxygen: 2
  • Hydrogen: 1
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Describe the hydroxy-group

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Describe the acid-group

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Describe the amino-group

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Describe the structure of an amino acid

A

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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is an aromatic ring?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Describe the methyl-group

A

A carbon and three hydrogen atoms bonded.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

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

A

Cannot

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

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

A

1Å = 10^-10 m

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the mass of 1 Dalton in kg?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

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

A

1 hydrogen atom

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the two most important properties of water?

A

Electric dipole moment and dielectric constant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Define electric dipole moment

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

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

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

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?)

A

2.95 D

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

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

A

1 D = 3.34 x 10^-30 Cm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

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, __.

A

Not uniform
Charge distribution
±q
r

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is the name for the bond between water molecules?

A

Hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the bond energy of a hydrogen bond?

A

U = 0.03 x 10^-18 J

28
Q

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

A

Four

29
Q

Define dielectric constant (also known as relative permittivity)

A

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

30
Q

What is the dielectric constant of water at 25ºC?

A

~80

31
Q

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

A

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

32
Q

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

A

Permanent electric dipole moment
Induced dipole moment

33
Q

Give the equation for an induced dipole moment

A

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

34
Q

Define induced dipole moment

A

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

35
Q

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

A

α’ = polarisability volume
ε_0 = permittivity of a vacuum

EXTRA: units: m^2

36
Q

What is the purpose of the Debye equation?

A

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.

37
Q

Give the Debye equation

A

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

38
Q

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

A

n_r = refractive index of water
ε_r = permittivity of water

39
Q

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

A

H2O
OH⁻
⁺H3O

40
Q

Why is water made up of multiple types of molecules?

A

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.

41
Q

What is the dissociation rate of water?

A

r_D = 2.5 x 10^-5 /s

42
Q

What is the molar concentration of water?

A

1000g / 18g/mol. = 55.6 mol/L

Mass of 1L of water / molar weight

43
Q

Define pH value

A

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

44
Q

Give the equation for the pH value of water

A

[ ] = molar concentration of positively charged complex

45
Q

Give the equation for the dissociation constant of water

A

K_D = dissociation constant

46
Q

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

A
47
Q

Give the equation for pH in terms of pK

A
48
Q

Define pK value

A

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

49
Q

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

A

Will equal

50
Q

Define Gibbs free energy

A

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.

51
Q

Give the equation for Gibbs free energy

A

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

52
Q

Define enthalpy

A

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.

53
Q

Define entropy

A

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.

54
Q

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

A

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

55
Q

Define amino acid

A

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

56
Q

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

A

R-COO⁻
H⁺

57
Q

What is the dissociation constant equation for an acid group?

A
58
Q

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

A
59
Q

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

A

NH2
NH3⁺

60
Q

Define nucleotide

A

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.

61
Q

What are the two purines?

A

Adenine
Guanine

62
Q

What are the three pyrimidines?

A

Cytosine
Uracil
Thymine

63
Q

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

A

Pyrimidines

64
Q

What are the base pair combinations for DNA?

A

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

65
Q

What are the base pair combinations for RNA?

A

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

PHYS3012: Molecular BioPhysics (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions