CBI Notes Flashcards
What does the letter Z represent?
Atomic number
What is the unit for atomic mass?
Dalton (Da)
Define ionisation energy
Energy to remove an electron
Define electron affinity
Energy change when you add an electron to an element in it’s ground state
Electronegativity
Power of an atom to attract electron (~ IE and EA average)
How many known elements are there?
118
What do quantum numbers describe?
Atomic orbitals
What are the 4 quantum numbers?
Principal (n)
Orbital (azimuthal) (l)
Magnetic (ml)
Spin (ms)
What does the principle (n) define?
Shell
What does the azimuthal (l) define?
Orbital shape (s, p, d or f)
What does the magnetic (ml) define?
Number and orientation of the orbital shapes in a subshell
What does the spin (ms) define?
Spin direction
How can quantum numbers be calculated?
Calculating the solutions to wave functions
What are the possible values of the azimuthal number?
l = 0, 1, 2… (n-1)
where n is the principal number
In which sub shell is an electron with l=0
s
In which sub shell is an electron with l=1
p
In which sub shell is an electron with l=2
d
In which sub shell is an electron with l=3
f
What are the potential values of the magnetic quantum number (ml)?
0, +/- 1, +/- 2, … +/- l
What is a degenerate subshell?
Subshells with equivalent energy despite varying orientation (i.e. px, py and pz are degenerate)
Define the Pauli Exclusion Principle
No 2 electrons can have the same set of four quantum numbers
Define the Aufbau Principle?
The lowest orbital (least energy) is first occupied
Define Hund’s Rule
Electrons will fill separate orbitals in the same subshell before pairing up, unpaired electrons will have the same spin
Define Madelung’s rule
Some energy levels have overlaps (i.e.: 4s < 3d)
Define electronegativity
The power of an atom to attract electrons to itself
Define a cation
+/ve ion
Define an anion
-/ve ion
How is an “ionic bond” (lattice) defines?
A bond where EN>2
What is the net effect of ionic bonding?
Ionic lattice
Define covalent bonding
Electrons in the outermost shell are shared
What is a bonded pair (covalent bonding)?
Shared e-
What is a lone pair (covalent bonding)
Unshared e-
What does a significant difference in electronegativity (but <2) suggest?
Polar covalent bonding
Define molecule (IUPAC definition)
A molecule is an electrically neutral entity consisting of more than one atom
Difference between molecular and empirical formula
Molecular indicates how many of each atom is present but empirical shows proportion
What is the convention in the order that elements in organic molecules are written?
C(x)H(y) and then alphabetical order
What is the convention in the order that elements in ions are written?
+/ve ion first, -/ve ion second
What are the conventions in the writing of oxides?
End with O
What are the conventions in the writing of acids?
Start with H
What are the conventions in the writing of hydroxides?
End with OH
What does the condensed structural formula suggest?
The order molecules are in
What does the skeletal formula represent?
The shape of bonds and only some explicit atoms (most Cs and Hs are implicit)
What is VESPR theory?
It is used to predict the 3D shape of a molecule
What is the tetrahedral bond angle?
109.5
What is the bonding angle with 4 electron domains but 1 is a lone pair (i.e.: ammonia)?
106.6
What is the bonding angle with 4 electron domains but 2 are lone pairs (i.e.: water)?
104.5
Which are more repulsive, bonding or lone pairs?
Lone pairs
Which type of bonds are present in a double bond?
1 sigma and 1 pi
Which type of bonds are present in a triple bond?
1 sigma and 2 pi
Which type of bonds are present in a single bond?
1 sigma
What is VB theory?
Valance bond theory is that bonding requires subatomic orbital hybridisation
What is MO theory?
Molecular orbital theory predicts bond lengths and energies bit is complex with larger molecules
How much is 1 mol?
6.02e23
What does high Ka (dissociation constant) suggest for an acid?
Strong
What does low Ka (dissociation constant) suggest for an acid?
Weak
What dissociation do strong acids have?
Full
What dissociation do weak acids have?
Weak
What combines well to produce a buffer?
A weak acid and it’s conjugate base or a weak base and it’s conjugate acid
Withing which range do buffers work?
pH ranges approximately similar (+/- 1) to their pKa
How is a buffer produced?
Weak acid + salt of that acid
Weak base + salt of that base
How many stereoisomers does a molecule have?
2^n
where n is the number of stereoisomers
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
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
Describe the optical activity of enantiomers
Equal and opposite
Describe Z isomerism
Higher priority molecules on the same side of a double bond
Describe E isomerism
Higher priority molecules on either side of the double bond
What are examples of non-covalent interactions?
Permanent dipoles
London dispersion forces
Hydrogen bonds
Ionic interactions
Hydrophobic interactions
Steric interactions
Which non-covalent forces are considered Van de Waals?
Permanent dipoles
London dispersion forces
Hydrogen bonds
Ionic interactions
What increases the size of a London dispersion force?
Larger molecule
Which molecules form hydrogen bonds?
F
N
O
Law of conservation of energy
Energy cannot be created or destroyed, only transferred from one form to another
What is true if delta G <0?
Spontaneous and exergonic
What is true if delta G >0?
Non spontaneous endergonic
What is true if delta G =0?
Chemical equilibrium
What change in enthalpy (H) do favourable reactions have?
Negative
What change in entropy (S) do favourable reactions have?
Positive
What does an equilibrium constant (K)>1 suggest?
Forward reaction favoured
What does an equilibrium constant (K)<1 suggest?
Backwards reaction favoured
What is the second law of thermodynamics?
The entropy of the entire universe will increase oover time
What does delta H>0 suggest?
Endothermic
What does delta H<0 suggest?
Exothermic
Which are the most common biological redox pairs?
NADH/NAD+ and FAD/FADH2
How is NAD+ reduced?
Nicotinamide ring acts as an e- acceptor
How is FAD reduced?
FAD ring acts as an e- acceptor
What do chemical catalysts do?
They lower the energy required to overcome the transition state by providing an alternative reaction pathway
What does delta S>0 suggest?
Increase in ways for energy to be dispersed
What does delta S<0 suggest?
Decrease in the ways for energy to be dispersed
What’s Hess’ Law?
Total enthalpy change for a given reaction is independent of reaction pathway
Which step of an SN1 reaction is rate determining?
The first step has the highest Ea
Which step of an SN2 reaction is rate determining?
It’s a one step reaction
Which type of substitution reaction has a carbocation intermediary?
SN1
Which type of substitution reaction may lead to stereoinversion?
SN2
Which type of substitution reaction is biologically more common?
SN2
What are the 4 major categories of biomolecules?
Sugars
Lipids
Nucleotides
Amino acids
What is the polymer of sugars?
Polysaccharide
What is the polymer of nuceleotides?
Nucleic acids
What is the polymer of amino acids?
Proteins
What is the general structure of carbohydrates?
(CH2O)n
What are the two types of monosaccharide?
Aldose
Ketose
In which form are carbohydrates found in water?
They can interconvert between ring and linear
How do monosaccharides bond?
Condensation reactions to form glycosidic linkages
Which are the lipid classes?
Fatty acid
Triacylglycerols
Sterol lipids
Glycerophospholipids
Sphinolipids
How would we write the name of a fatty acid with 18 carbons and 3 double bonds?
18:3
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
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)
Which lipid is common in adipocytes?
Triacylglyerols
Which lipid is common in membranes?
Glycerophospholipids
What is true about flip-flop in accordance with the Singer model?
It’s unfavourable and rare
Which phase do saturated lipids favour in the membrane?
Solid
Which phase do unsaturated lipids favour in the membrane?
Liquid
How does cholesterol regulate membrane fluidity?
Stabilises at high temp
Prevents stiffening at low temp
What is Tm?
The temperature at which membranes transition between solid and liquid phases
What type of bond forms between guanine and cytosine?
Triple hydrogen bond
What type of bond forms between adenine and thymine/ uracil?
Double hydrogen bond
Give examples of monomeric nucleotides?
ATP and GTP
How do nucleotides bond to form DNA?
Condensation reaction
Bonds form between the 3C and phosphate group
What groups are present in an amino acid?
R group
COOH carboxyl
NH2 amine group
What are the 4 classifications of amino acid?
Neutral, non-polar
Neutral, polar
Basic
Acidic
What does the primary protein structure define?
Structure and function
What bonds form in primary protein structure?
Peptide (-CO-NH-) bonds
What bonds form in secondary protein structures?
H interactions (between carbonyl and nitrogen atoms)
What are the potential secondary structures of polypeptides?
Beta sheets
Alpha helices
Hairpin bends
Beta turns
What determines tertiary folding of a protein?
R group interactions
What determines quaternary interactions?
Additional polymers/ molecules
Name 4 protein purification techniques
SEC (size-exclusion chromatography)
IEC (ion-exchange chromatography)
Affinity chromatography
SDS-PAGE
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.
Describe IEC
IEC (ion-exchange chromatography) passes liquid through a column which has beads treated to certain charges to interact with proteins passing through
Describe affinity chromatography
Tags in a column interact with the matrix which traps the proteins in the column. This can later be washed out
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
Hiii
<3
What is the function of biological catalysts?
Lower the energetic barrier to allow a reaction to proceed
Where can Delta G be shown on a reaction pathway?
Instead if Ea
How do we classify enzyme names?
By 4 numbers
What is Vmax?
The point at which all enzymes are occupied by substrates
What is Km ?
A constant which defines the catalytic properties of an enzyme
What is the Michaellis-Menten equation?
An equation which describes the variation of enzyme activity as a function of substrate concentration
What does a high KM suggest about substrate affinity?
Low as a lot of substrate is required to reach Vmax
What does a low KM suggest about substrate affinity?
High as a small concentration of substrate is required to reach Vmax
What do Lineweaver-Burk plots show?
A double reciprocal of a Michaelis Menten plot which allows us to calculate Vmax ad KM
How is a Lineweaver-Burk plot used to calculate Vmax?
The y-intercept is 1/Vmax
How is a Lineweaver Burk plot used to calculate KM?
The root = -1/KM
What is k(cat)?
The max turnover of a saturated enzyme/second
What does a high k(cat) suggest?
Greater efficiency
What dies a low k(cat) suggest?
Lower efficieny
Describe a competitive inhibitor
Resembles the substrate but can be overcome by a higher substrate concentration
Describe an uncompetitive inhibitor
Binds to the formed complex and prevents product release and cannot be overcome
Describe a non-competitive inhibitor
Binds to the allosteric site and prevents catalyst if function
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)
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)
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)
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.
Why do high temperatures denature enzymes?
Break tertiary and secondary structure bonds
What type of inhibition is allosteric?
Primarily non-competitive but other kinds can be too
What shape is the Michaelis Menten enzymatic profile for allosteric-regulated enzymes?
Sigmoidal due to high sensitivity
Where does the Kreb’s cycle occur?
Mitochondrial matrix
Which part of respiration is anaerobic?
Glycolysis
Where does glycolysis occur?
Cytosol
What are the steps in respiration?
Glycolysis
Oxidative decarboxylation
TCA
ETC
OXPHOS
What are the steps in oxidative decarboxylation?
Decarboxylation
Oxidation
Transfer to CoA
What enzyme catalyses oxidative carboylation?
Pyruvate dehydrogenase
Where does glycolysis occur?
Cytosol
Where does glucogenesis occur?
Primarily in the Cytosol
Define glycolysis
The breakdown of glucose resulting in the production of two pyruvate molecules
What are the steps in glycolysis?
Trapping glucose
Cleavage into 3C unit
Pay-off
Which steps in glycolysis are not reversible?
Step 1: 1 and 3
Step 3: last step
