Lecture 1 Flashcards
(153 cards)
1
Q
Define electronegativity
A
The ability of an atom to attract the bonding pair of electrons in a covalent bond.
2
Q
What indicates how easily an electron will be transferred between atoms ?
A
The electronegativity of the atoms.
3
Q
What is meant by the term ‘Transient interactions’?
A
Protein interactions which are easily formed and broken.
4
Q
Define hydrophobic
A
Molecules which repel water and cannot make dipolar interactions.
5
Q
Give some properties of hydrophobic molecules.
A
Cannot make dipolar interactions.
Non-polar molecules
6
Q
Are non-polar molecules hydrophobic or hydrophilic?
A
Hydrophobic
7
Q
What is meant by a molecule being hydrophilic?
A
Can make ionic or hydrogen bonds with water.
8
Q
Are hydrophilic molecules usually polar or non-polar?
A
Polar
9
Q
Are polar molecules hydrophobic or hydrophilic?
A
Hydrophilic
10
Q
What are intramolecular interactions?
A
Interactions between separate parts of the same molecule.
11
Q
What are intermolecular interactions?
A
Interactions between different molecules.
12
Q
What are the properties of water?
A
Transient interactions
Hydrophobic and hydrophilic regions.
Strong covalent bonds.
13
Q
Label a Eukaryotic cell
A
-
14
Q
Draw the structure of a water molecule
A
-
15
Q
What is the energy range of a covalent bond in KJ/mol ?
A
150-1000
16
Q
What is the energy of an ionic bond in KJ/mol?
A
250
17
Q
What is the energy of Dispersion forces in KJ/mol?
A
2
18
Q
What is the energy of Dipole Dipole interactions in KJ/mol?
A
2
19
Q
What is the energy of a hydrogen bond in KJ/mol?
A
20
20
Q
When is a covalent bond non-polar?
A
When the bonding pair of electrons are equally shared between each atom.
21
Q
Name all the types of non-covalent interactions.
A
Dispersion forces. Permanent Dipolar interactions (Dipole Dipole). Steric Repulsion. Hydrogen bonds. Ionic interactions. Hydrophobic forces.
22
Q
Name the features of Dispersion forces.
A
Weak
Occur between all molecules.
Rely on areas of opposite charges. (Temporary dipoles).
Aways occur but are transient.
23
Q
What type of molecules do dispersion forces occur between?
A
All molecules of opposite charges or with temporary opposite dipoles.
24
Q
Describe the relative strength of dispersion forces.
A
Weak and transient
25
What distance so steric repulsion forces act over?
Short
26
What type of molecules do Permanent dipole interactions occur between?
Between opposite partial charges on polar molecules.
27
What do hydrogen bonds rely on?
The presence of Fluorine, oxygen and Nitrogen.
28
Describe the solubility of molecules based on their ability to form hydrogen bonds with water.
Can form hydrogen bonds with water - soluble in water.
| Can't form hydrogen bonds with water- not soluble in water.
29
Where on a molecule do allosteric enzymes bind?
A site that is not the active site.
30
How do allosteric enzymes affect the molecule they are bound to?
They cause a change in the active site.
31
What are the 2 types of allosteric enzyme?
Repressors and Activators
32
How do activator allosteric enzymes affect the molecule they are bound to?
Restore the original active site of the molecule.
33
How do repressor allosteric enzymes affect the molecule they are bound to?
Disrupt the active site of the molecule, causing it to change.
34
When are repressor allosteric enzymes active?
When signalling molecules are not preset.
35
When are activator allosteric enzymes present?
When signalling molecules are present.
36
Draw the structure of a Hydroxyl group
-
37
Draw the structure of carboxylic acid
-
38
What is the R group variant of an amino acid.
The variable region of each amino acid.
39
What are the main functional groups of the amino acid?
Amine Group
Carboxyl Group
R group
Hydrogen
40
Draw the structure of an amino acid
-
41
What is a condensation reaction?
2 molecules join to form a single molecule. Water is produced as a bi-product of the bond formation.
42
What is a hydrolysis reaction?
Breakdown of a chemical bond using water.
43
What is Rosalind Franklin famous for?
She contributed to finding the structure of DNA using X-ray diffraction.
44
What is a molecule called when it has both Hydrophilic and hydrophobic regions?
Amphipathic
45
What is meant by a molecule being amphipathic?
The molecule has both hydrophobic and hydrophilic regions.
46
Draw a carboxylic acid
-
47
Draw the structure of Glycerol
-
48
Draw the structure of an ester bond
-
49
Draw the Structure of a phospholipid
-
50
How do the Phospholipids in the cell membrane affect cellular shape?
The hydrophilic heads face outwards towards the aqueous fluid whilst the hydrophilic fatty acid tails face inwards towards each other.
If the phospholipids have a small tail this creates a micelle (small, single-layered sphere). But if they have large tails, this creates a Liposome.
51
What is a micelle?
A small, single-layered sphere of phospholipids.
52
What is a Liposome?
A sphere of at least one lipid bilayer with a hollow centre.
53
What are the issues of using an extremely high concentration of liquid to do U.V spectrophotometry?
Light cannot pass through the substance and so no absorbency reading can be determined.
54
What must be a feature of the liquid sample used in U.V. spectrometry?
To be in perfect Brownian motion.
55
What is Brownian motion?
Random, uncontrolled movement of particles in a fluid as they constantly collide with other molecules.
56
Why is having a low concentration sample in U.V. spectrophotometry an issue?
Insufficient molecules to reliably determine the absorbent of a substance.
57
What are steric interactions?
Repulsion between valence electrons of adjacent atoms or non-bonded atoms.
58
Is water polar are non-polar?
Polar
59
If a molecule cannot form hydrogen bonds, what does this mean about its properties?
It will not be soluble in water.
60
If a molecules is not soluble in water, what type of bonds will it be unable to make?
Hydrogen
61
What would happen to a cell if you froze it and why?
The cell would lyse (burst). This is the case because the main component of the cell is water, which expands when frozen.
62
If all bonds were permanent and covalent, what would happen to a cell?
Cells would die because the bonds would not be able to be broken and so many metabolic pathways would be ceased.
63
Between what type of molecules does hydrophilic interactions occur?
Polar hydrophiles
64
Are hydrophilic interactions polar or non-polar?
Polar
65
Give an example of a molecule which has hydrophilic interactions.
Glucose
66
Name some hydrophileis
Ammonia, alcohol, urea
67
What are hydrophileis?
Molecules which can make hydrogen bonds.
68
What type of bond is a hydrogen bond?
Dipole-dipole
69
What atoms do hydrogen bonds form between ?
H and N,O or F
70
What is the relative strength of hydrogen bonds compared to covalent bonds.
They have about 1/10th the strength of covalent bonds.
71
What type of molecules can ionic bonds form between.
Between 2 oppositely charged ions = pure ionic.
Between covalent molecules with positively and negatively charged areas.
72
What does the strength of an ionic bond depend on?
The electrostatic charge density of the interacting ions
73
Give an example of an ionic compound.
NaCl
74
What is the average bond energy of an ionic bond?
250Kj/mol
75
Give example of hydrophone molecules.
Alkanes, oils, fats
76
List these bond interactions from strongest to weakest:
```
Dipole-dipole
Dispersion forces
Ionic
Dipole-Induced Dipole
Covalent
Hydrogen
```
```
Ionic
Covalent
Hydrogen
Dipole-Dipole
Dipole- Induced Dipole
Dispersion forces
```
77
Describe the distance that steric repulsion acts over
Very short
78
How does steric interaction alter the availibility of one molecule to another.
Increases it by opening bond angles.
79
Why do dipoles form within molecules?
Uneven electron distribution
80
Why do some molecules with polar bonds have no overall dipole?
They are symmetrical so their dipoles cancel out.
81
What type of molecules do dispersion forces occur between ?
All
82
What type of bonds are dispersion forces?
Covalent
83
How do disulphide bonds form?
The Sulfhydryl group of one cysteine acts as a nucleophile and attacks the side chain of a second cysteine residue. This forms a disulphide bridge during an oxidation reaction.
84
What reaction type is used to form disulphide bridges?
Oxidation
85
How are disulphide bridges beneficial to proteins?
They help structure the protein (tertiary) and prevent degradation.
86
In general terms, what is a covalent compound ?
A covalent compound equally shares one or more pairs of electrons.
87
In general terms, what is an ionic compound?
One or more electrons are transferred from one atom to the other.
88
What are chemically inert atoms?
Atoms which electrons are very tightly associated with itself and therefore cannot interact with other atoms
89
How does the electronegativity of atoms indicate the type of bonding that they will undergo?
Large difference in electronegativity = ionic.
Small difference = covalent bonding
90
Why does a large difference in electronagetivity between 2 atoms indicate ionic bonding will occur?
Suggests that one atom has the attractive ability to be able to tear an electron away from the other atom.
91
What must the difference in electronegativity be greater than or equal to for ionic bonding to occur?
1.7
92
What type of bonding occurs between 2 of the same atoms and why?
Covalent - there is no difference in electronegativity
93
What is the general formation of ionic compounds called?
Lattices
94
What is the general formation of covalent compounds called?
Molecules
95
What is the overall charge of an ionic compound?
Neutral
96
What is the overall charge of a covalent compound?
Neutral
97
What are lone pairs of electrons?
Refers to covalent bonding.
| Pairs of electrons which are not shared of used to form chemical bonds.
98
How many lone pairs of electrons does ammonia have?
1
99
What is a dative covalent bond?
The shared pair of electrons in a covalent bond are donated by one atom only.
100
What is another name for a dative covalent bond?
Coordinate bond
101
What sign is used to indicate a dative covalent bond?
An arrow
102
How many covalent and dative covalent bonds does NH4 have?
3 covalent
| 1 Dative
103
In the dative covalent bond in NH4, which atom donates 2 electrons?
N
104
What must be true for atoms to share electrons and form covalent bonds?
Valence orbitals must overlap
105
What are formed when atomic orbitals overlap?
New molecular orbitals
106
What type of orbitals must be present to allow covalent bonds to form?
Bonding molecular orbitals
107
What type of orbitals inhibit covalent bond formation?
Non-bonding molecular orbitals
108
What must be true about the number of electrons in the bonding and anti bonding molecular orbitals of an atom for covalent bonding to occur?
More electrons in bonding orbital than anti bonding orbital.
109
Do bonding or anti-bonding molecular orbitals have a greater energy?
Anti-bonding orbitals have a greater energy level
110
What is the benefit of bonding molecular orbitals having lower energy levels than anti bonding molecular orbitals?
They are more stable
111
What type of electrons are detected by U.V-visible spectrophotometry?
Movement of electrons from bonding into anti-bonding orbitals upon excitation is detected.
112
What are non-bonding molecular orbitals?
Orbitals which are occupied by non-bonding non-bonding valence electron pairs.
113
What are the two different type of molecular orbitals?
Sigma and Pie
114
How can a sigma orbital be easily identified from a pi orbital?
The pie orbitals have 2 lobes, sigma orbitals only have 1 lobe
115
What is formed when an electron pair is shared in a pi orbital?
Pi bond
116
What molecular orbitals are used when a single covalent bond is formed?
only the sigma orbital
117
What molecular orbitals are used when a double covalent bond is formed.
Sigma and pi
118
What must be the valency of an atom to create a double covalent bond?
Greater than or equal to 2
119
In a triple covalent bond, how many pairs of electrons are shared in each molecular orbital?
1 in the sigma orbital
| 2 in the pi orbital
120
What valency is required for an atom to forma triple covalent bond?
Greater than or equal to 3
121
What type of expansion occurs in hyper valency?
Octet
122
What is hyper valency?
An atom having more than 8 valence electrons.
123
Give an example of a hypervalent atom
Phosphorus
124
Name some elements which can have valence variability
Phosphorus
| Sulfur
125
What causes hypervalency?
Electron pairs participating in more than one bond
126
What are the possible valencies of sulphur?
2 and 6
127
What type of bonding is present in a benzene ring ?
Conjugate
128
What type of molecule do all aromatic compounds contain?
A benzene ring
129
What are non-aromatic compounds called?
Aliphatic
130
How does conjugate bonding occur in a ring?
The p orbitals of 6 carbons overlap to form a continuous, single pi orbital. The 6 valence electrons in the pi orbital are delocalised and cause the ring to have half double and half single alternating bonds.
131
What are resonance hybrid covalent bonding molecules?
They have delocalised valence electrons but no conjugate system.
132
Give an example of a resonance hybrid molecule
O3
133
Show the resonance hybrid bonding in O3
O-O=O
134
What are polyatomic ionic compounds?
compounds which contain both ionic and covalent bonds
135
Give an example of a polyatomic ionic compound
CaCO3
| Na2SO4
136
What overall causes covalent bonds to become polar?
The uneven distribution of shared electrons due to difference in the electronegativity of atoms sharing the electrons.
137
For a covalent bond to be non-polar, describe the difference in electronegativity of the atoms sharing the electrons
Same electronegativity
138
What is the term used to describe the difference in the positive and negative dipole charges of a molecule?
Dipole moment
139
What type of molecular interaction occurs between all molecules?
Dispersion forces
140
Describe the length of time that a dispersion force usually exists for.
Very short lived
| 10^-16s
141
Why are dispersion forces so short lived?
The electrons are constantly moving within their orbitals and altering the induced dipoles.
142
Describe the distance that dispersion forces act over.
Short
143
How does shape of molecules affect strength of dispersion forces?
Molecules that are able to fit closer together have stronger dispersion forces as their opposite charges are in closer proximity and able to create stronger interactions.
144
How does size of molecules affect strength of dispersion forces?
The large the molecule, the greater the dispersion forces because there are more electrons present.
145
What is the weakest type of non-covalent bond?
Dispersion forces
146
Define van der Waals forces.
The overall interaction between molecules when taking into account their dispersion forces, dipolar force and steric repulsion forces.
147
In what environment would attractive forces between molecules be strongest ?
In a vacuum
148
What is a hydrogen bond donor?
The electronegative atom that the hydrogen atom is bonded to
149
What is a hydrogen bond acceptor?
An atom which is bonded to hydrogen via a non-bonding pair of electrons.
150
How does the arrangement of atoms in a 'H' bond affect bond strength.
All of the nuclei of atoms in the 'H' bond must be on a straight line for maximum bond strength.
151
What is a 'salt bridge'?
An ionic bond between 2 oppositely charged amino acid side chains.
152
What is used to stabilise hydrophobic interactions?
Dispersion forces
153
When do van Der walls forces appear?
When the charge distribution of any atom isn't symmetrical
