CBI Notes Flashcards
(165 cards)
1
Q
What does the letter Z represent?
A
Atomic number
2
Q
What is the unit for atomic mass?
A
Dalton (Da)
3
Q
Define ionisation energy
A
Energy to remove an electron
4
Q
Define electron affinity
A
Energy change when you add an electron to an element in it’s ground state
5
Q
Electronegativity
A
Power of an atom to attract electron (~ IE and EA average)
6
Q
How many known elements are there?
A
118
7
Q
What do quantum numbers describe?
A
Atomic orbitals
8
Q
What are the 4 quantum numbers?
A
Principal (n)
Orbital (azimuthal) (l)
Magnetic (ml)
Spin (ms)
9
Q
What does the principle (n) define?
A
Shell
10
Q
What does the azimuthal (l) define?
A
Orbital shape (s, p, d or f)
11
Q
What does the magnetic (ml) define?
A
Number and orientation of the orbital shapes in a subshell
12
Q
What does the spin (ms) define?
A
Spin direction
13
Q
How can quantum numbers be calculated?
A
Calculating the solutions to wave functions
14
Q
What are the possible values of the azimuthal number?
A
l = 0, 1, 2… (n-1)
where n is the principal number
15
Q
In which sub shell is an electron with l=0
A
s
16
Q
In which sub shell is an electron with l=1
A
p
17
Q
In which sub shell is an electron with l=2
A
d
18
Q
In which sub shell is an electron with l=3
A
f
19
Q
What are the potential values of the magnetic quantum number (ml)?
A
0, +/- 1, +/- 2, … +/- l
20
Q
What is a degenerate subshell?
A
Subshells with equivalent energy despite varying orientation (i.e. px, py and pz are degenerate)
21
Q
Define the Pauli Exclusion Principle
A
No 2 electrons can have the same set of four quantum numbers
22
Q
Define the Aufbau Principle?
A
The lowest orbital (least energy) is first occupied
23
Q
Define Hund’s Rule
A
Electrons will fill separate orbitals in the same subshell before pairing up, unpaired electrons will have the same spin
24
Q
Define Madelung’s rule
A
Some energy levels have overlaps (i.e.: 4s < 3d)
25
Define electronegativity
The power of an atom to attract electrons to itself
26
Define a cation
+/ve ion
27
Define an anion
-/ve ion
28
How is an "ionic bond" (lattice) defines?
A bond where EN>2
29
What is the net effect of ionic bonding?
Ionic lattice
30
Define covalent bonding
Electrons in the outermost shell are shared
31
What is a bonded pair (covalent bonding)?
Shared e-
32
What is a lone pair (covalent bonding)
Unshared e-
33
What does a significant difference in electronegativity (but <2) suggest?
Polar covalent bonding
34
Define molecule (IUPAC definition)
A molecule is an electrically neutral entity consisting of more than one atom
35
Difference between molecular and empirical formula
Molecular indicates how many of each atom is present but empirical shows proportion
36
What is the convention in the order that elements in organic molecules are written?
C(x)H(y) and then alphabetical order
37
What is the convention in the order that elements in ions are written?
+/ve ion first, -/ve ion second
38
What are the conventions in the writing of oxides?
End with O
39
What are the conventions in the writing of acids?
Start with H
40
What are the conventions in the writing of hydroxides?
End with OH
41
What does the condensed structural formula suggest?
The order molecules are in
42
What does the skeletal formula represent?
The shape of bonds and only some explicit atoms (most Cs and Hs are implicit)
43
What is VESPR theory?
It is used to predict the 3D shape of a molecule
44
What is the tetrahedral bond angle?
109.5
45
What is the bonding angle with 4 electron domains but 1 is a lone pair (i.e.: ammonia)?
106.6
46
What is the bonding angle with 4 electron domains but 2 are lone pairs (i.e.: water)?
104.5
47
Which are more repulsive, bonding or lone pairs?
Lone pairs
48
Which type of bonds are present in a double bond?
1 sigma and 1 pi
49
Which type of bonds are present in a triple bond?
1 sigma and 2 pi
50
Which type of bonds are present in a single bond?
1 sigma
51
What is VB theory?
Valance bond theory is that bonding requires subatomic orbital hybridisation
52
What is MO theory?
Molecular orbital theory predicts bond lengths and energies bit is complex with larger molecules
53
How much is 1 mol?
6.02e23
54
What does high Ka (dissociation constant) suggest for an acid?
Strong
55
What does low Ka (dissociation constant) suggest for an acid?
Weak
56
What dissociation do strong acids have?
Full
57
What dissociation do weak acids have?
Weak
58
What combines well to produce a buffer?
A weak acid and it's conjugate base or a weak base and it's conjugate acid
59
Withing which range do buffers work?
pH ranges approximately similar (+/- 1) to their pKa
60
How is a buffer produced?
Weak acid + salt of that acid
Weak base + salt of that base
61
How many stereoisomers does a molecule have?
2^n
where n is the number of stereoisomers
62
What are the Cahn-Ingol-Prelog rules for naming enantiomers?
- Assign priority (Z) based on atomic weight
- If there is a tie go out to the next furthest atom
- The lowest priority faces into the paper
- If the others are arranged clockwise -> R
- If the others are arranged anticlockwise -> S
63
What is the CORN rule for naming amino acid enantiomers?
- Orientate the molecule such that the H on the central C faces into the page
- Other groups face outward
- If they spell CORN clockwise they are D amino acids, if they spell it anticlockwise they are L
64
Describe the optical activity of enantiomers
Equal and opposite
65
Describe Z isomerism
Higher priority molecules on the same side of a double bond
66
Describe E isomerism
Higher priority molecules on either side of the double bond
67
What are examples of non-covalent interactions?
Permanent dipoles
London dispersion forces
Hydrogen bonds
Ionic interactions
Hydrophobic interactions
Steric interactions
68
Which non-covalent forces are considered Van de Waals?
Permanent dipoles
London dispersion forces
Hydrogen bonds
Ionic interactions
69
What increases the size of a London dispersion force?
Larger molecule
70
Which molecules form hydrogen bonds?
F
N
O
71
Law of conservation of energy
Energy cannot be created or destroyed, only transferred from one form to another
72
What is true if delta G <0?
Spontaneous and exergonic
73
What is true if delta G >0?
Non spontaneous endergonic
74
What is true if delta G =0?
Chemical equilibrium
75
What change in enthalpy (H) do favourable reactions have?
Negative
76
What change in entropy (S) do favourable reactions have?
Positive
77
What does an equilibrium constant (K)>1 suggest?
Forward reaction favoured
78
What does an equilibrium constant (K)<1 suggest?
Backwards reaction favoured
79
What is the second law of thermodynamics?
The entropy of the entire universe will increase oover time
80
What does delta H>0 suggest?
Endothermic
81
What does delta H<0 suggest?
Exothermic
82
Which are the most common biological redox pairs?
NADH/NAD+ and FAD/FADH2
83
How is NAD+ reduced?
Nicotinamide ring acts as an e- acceptor
84
How is FAD reduced?
FAD ring acts as an e- acceptor
85
What do chemical catalysts do?
They lower the energy required to overcome the transition state by providing an alternative reaction pathway
86
What does delta S>0 suggest?
Increase in ways for energy to be dispersed
87
What does delta S<0 suggest?
Decrease in the ways for energy to be dispersed
88
What's Hess' Law?
Total enthalpy change for a given reaction is independent of reaction pathway
89
Which step of an SN1 reaction is rate determining?
The first step has the highest Ea
90
Which step of an SN2 reaction is rate determining?
It's a one step reaction
91
Which type of substitution reaction has a carbocation intermediary?
SN1
92
Which type of substitution reaction may lead to stereoinversion?
SN2
93
Which type of substitution reaction is biologically more common?
SN2
94
What are the 4 major categories of biomolecules?
Sugars
Lipids
Nucleotides
Amino acids
95
What is the polymer of sugars?
Polysaccharide
96
What is the polymer of nuceleotides?
Nucleic acids
97
What is the polymer of amino acids?
Proteins
98
What is the general structure of carbohydrates?
(CH2O)n
99
What are the two types of monosaccharide?
Aldose
Ketose
100
In which form are carbohydrates found in water?
They can interconvert between ring and linear
101
How do monosaccharides bond?
Condensation reactions to form glycosidic linkages
102
Which are the lipid classes?
Fatty acid
Triacylglycerols
Sterol lipids
Glycerophospholipids
Sphinolipids
103
How would we write the name of a fatty acid with 18 carbons and 3 double bonds?
18:3
104
How do we describe the location of a double bond in a fatty acid which is 6 carbons from the end CH3?
w-6 or n-6
105
How do we describe the location of a double bond in a fatty acid which is 6 carbons from the COOH?
18:1(6) or C-6
(in an 18 C and 1 double bond chain)
106
Which lipid is common in adipocytes?
Triacylglyerols
107
Which lipid is common in membranes?
Glycerophospholipids
108
What is true about flip-flop in accordance with the Singer model?
It's unfavourable and rare
109
Which phase do saturated lipids favour in the membrane?
Solid
110
Which phase do unsaturated lipids favour in the membrane?
Liquid
111
How does cholesterol regulate membrane fluidity?
Stabilises at high temp
Prevents stiffening at low temp
112
What is Tm?
The temperature at which membranes transition between solid and liquid phases
113
What type of bond forms between guanine and cytosine?
Triple hydrogen bond
114
What type of bond forms between adenine and thymine/ uracil?
Double hydrogen bond
115
Give examples of monomeric nucleotides?
ATP and GTP
116
How do nucleotides bond to form DNA?
Condensation reaction
Bonds form between the 3C and phosphate group
117
What groups are present in an amino acid?
R group
COOH carboxyl
NH2 amine group
118
What are the 4 classifications of amino acid?
Neutral, non-polar
Neutral, polar
Basic
Acidic
119
What does the primary protein structure define?
Structure and function
120
What bonds form in primary protein structure?
Peptide (-CO-NH-) bonds
121
What bonds form in secondary protein structures?
H interactions (between carbonyl and nitrogen atoms)
122
What are the potential secondary structures of polypeptides?
Beta sheets
Alpha helices
Hairpin bends
Beta turns
123
What determines tertiary folding of a protein?
R group interactions
124
What determines quaternary interactions?
Additional polymers/ molecules
125
Name 4 protein purification techniques
SEC (size-exclusion chromatography)
IEC (ion-exchange chromatography)
Affinity chromatography
SDS-PAGE
126
Describe SEC
SEC (size-exclusion chromatography) consists of passing a liquid through a column of porous beads, the smaller molecules will take longer as they will enter the pores but the larger molecules will pass through faster.
127
Describe IEC
IEC (ion-exchange chromatography) passes liquid through a column which has beads treated to certain charges to interact with proteins passing through
128
Describe affinity chromatography
Tags in a column interact with the matrix which traps the proteins in the column. This can later be washed out
129
Describe SDS-PAGE
Molecules are treated by with SDS detergent to make them -/ve. They are then placed between the anode (+) and cathode (-) and they travel towards the anode with the smallest arriving last
130
Hiii
<3
131
What is the function of biological catalysts?
Lower the energetic barrier to allow a reaction to proceed
132
Where can Delta G be shown on a reaction pathway?
Instead if Ea
133
How do we classify enzyme names?
By 4 numbers
134
What is Vmax?
The point at which all enzymes are occupied by substrates
135
What is Km ?
A constant which defines the catalytic properties of an enzyme
136
What is the Michaellis-Menten equation?
An equation which describes the variation of enzyme activity as a function of substrate concentration
137
What does a high KM suggest about substrate affinity?
Low as a lot of substrate is required to reach Vmax
138
What does a low KM suggest about substrate affinity?
High as a small concentration of substrate is required to reach Vmax
139
What do Lineweaver-Burk plots show?
A double reciprocal of a Michaelis Menten plot which allows us to calculate Vmax ad KM
140
How is a Lineweaver-Burk plot used to calculate Vmax?
The y-intercept is 1/Vmax
141
How is a Lineweaver Burk plot used to calculate KM?
The root = -1/KM
142
What is k(cat)?
The max turnover of a saturated enzyme/second
143
What does a high k(cat) suggest?
Greater efficiency
144
What dies a low k(cat) suggest?
Lower efficieny
145
Describe a competitive inhibitor
Resembles the substrate but can be overcome by a higher substrate concentration
146
Describe an uncompetitive inhibitor
Binds to the formed complex and prevents product release and cannot be overcome
147
Describe a non-competitive inhibitor
Binds to the allosteric site and prevents catalyst if function
148
How do KM and Vmax change in the presence of a competitive inhibitor?
Apparent increase in KM
No change in Vmax
(A higher substrate concentration is required for the same reaction)
149
How do KM and V max change in the presence of an uncompetitive inhibitor?
Apparent decrease in KM and Vmax by the sane extent
(As ESI complex is forming but not being release)
150
What is the effect of a non-competitive inhibitor on KM and Vmax?
KM stays the same
Vmax decreases
(less e=substrate is available to complete it’s function)
151
When may cofactors be important in catalytic activity?
These are vitamin-derived organic molecules such as NAD+ or FAD which may be necessary to initiate catalytic activity.
152
Why do high temperatures denature enzymes?
Break tertiary and secondary structure bonds
153
What type of inhibition is allosteric?
Primarily non-competitive but other kinds can be too
154
What shape is the Michaelis Menten enzymatic profile for allosteric-regulated enzymes?
Sigmoidal due to high sensitivity
155
Where does the Kreb’s cycle occur?
Mitochondrial matrix
156
Which part of respiration is anaerobic?
Glycolysis
157
Where does glycolysis occur?
Cytosol
158
What are the steps in respiration?
Glycolysis
Oxidative decarboxylation
TCA
ETC
OXPHOS
159
What are the steps in oxidative decarboxylation?
Decarboxylation
Oxidation
Transfer to CoA
160
What enzyme catalyses oxidative carboylation?
Pyruvate dehydrogenase
161
Where does glycolysis occur?
Cytosol
162
Where does glucogenesis occur?
Primarily in the Cytosol
163
Define glycolysis
The breakdown of glucose resulting in the production of two pyruvate molecules
164
What are the steps in glycolysis?
Trapping glucose
Cleavage into 3C unit
Pay-off
165
Which steps in glycolysis are not reversible?
Step 1: 1 and 3
Step 3: last step
