LSM1101 Notes

These notes have been made with the help of the slides from NUS professors. Dr
Takao, Dr Deng and Dr Ban.

Terms
1. Amphipathic
a. Molecule has both hydrophilic and hydrophobic groups, and can
interact with, water, other hydrophobic groups, and organic solvents
2. Amphoteric
a. Molecule has the ability to accept and donate protons

Solubility
1. Hydrogen bond occurs between a hydrogen atom with a partial positive
charge, and an oxygen with a partial negative charge
a. It is weak and easily broken
i. Holds ice in a hexagonal structure when cold enough
ii. Easily formed and broken when water is liquid
b. Water can form 4 hydrogen bonds
i. Each oxygen can form 2, each hydrogen can form 1
2. Solubility of compounds depends on how they interact with water
molecules
a. Hydrophilic molecules form strong bonds with water and dissolve
easily
b. Hydrophobic molecules do not form strong bonds with water and
resists dissolution
3. Ionic compounds consists of ions that interact with water to form hydration
shells
a. Electrostatic interactions between charged ions and partial charges
of water
b. Enough energy released to overcome water-water bonds and ion-ion
bonds
4. Polar molecules have hydrophilic groups that have partial charges to form
hydrogen bonds with water.
a. The hydrophilic groups may have stronger partial charges due to
the electronegativity of the rest of the molecule.
b. Hydration shell forms allowing dissolution
5. Non-polar molecules are hydrophobic due to their inability to interact with
water and thus do not dissolve easily in water.
a. The lack of hydrogen bonds causes the formation of a clathrate
structure around non-polar solutes that manage to dissolve
i. Clathrate is a cage-like arrangement of water molecules
around the solvent
ii. Clathrate formation is not energetically favoured and do not
easily form, leading to insolubility of solute.
b. Hydrophobic interaction occurs, where hydrophobic molecules
clump together to reduce the surface area exposed to water,
leading to a lower energy state.
i. Minimises clathrates formation, as they are smaller and
required less water molecules, and is thus favoured over
scattered hydrophobic solutes.

ii. Only observed in aqueous environment, as this minimises

interaction with water.
iii. This is not due to attractive forces like Van der Waals, but due
to the system trying to reach the lowest energy state.
6. Amphipathic molecules have both hydrophilic and hydrophobic groups
a. Their interaction with other molecules and water gives rise to
complex structures
i. Hydrophobic regions clump together to minimise exposure to
water
ii. Hydrophilic regions are exposed to water
7. Proteins tend to be amphipathic as it gives a stable structure
a. Hydrophilic surface allows dissolution in water found in most cells
b. Hydrophobic core maintains protein shape through hydrophobic
interactions

pH and Buffers
1. pH =

+
H

lg

a.

+
H

O H

K w =

b.

pH+ pOH = p K w

at 298 Kelvin

2. Human healthy pH is around 7.4

a. pH is maintained constant by homeostasis
b. Needs to remain constant to provide optimum environment for
enzyme function required for life
3. Enzymes at different locations in the body operate best at different pH
a. Stomach enzymes require an acidic medium
4. Bronsted-Lowry definition uses protons as reference instead of electrons
(Lewis)
a. Acids are proton donors, dissociating H+, producing conjugate base
b. Bases are proton acceptors, associate with H +, producing conjugate
acid
5. Ka is a measure of the strength of an acid
a. The smaller the Ka, the weaker the acid
i. The closer the pKa to 14, the weaker the acid
ii. Negative pKa indicates that the acid is a strong acid

6. Henderson-Hasselbalch equation:

[ HA ]

pH= p k a +lg

a. Not applicable when A- or HA concentration is near 0

7. When mixing weak acid and its conjugate base
a. Assume that further dissociation is negligible
b. Use Henderson-Hasselbalch equation to find pH
8. Buffers resists changes in pH by reacting away excess H + or OH- added
9. Buffering capacity is

pH= p K a 1

a. When equal concentrations of acid and conjugate base are present

10.Polyprotic acids have multiple buffering capacities
11.The human body has several buffers
a. Phosphate system (HPO42-/H2PO4-)
i. Protects pH of intracellular and extracellular environment
b. Bicarbonate system (HCO3-/H2CO3)
i. Protects pH of blood

ii. Breathing adjusts CO2 concentration, affecting H2CO3

concentration
c. Amino acids and proteins
i. Minor contribution to pH homeostasis

Amino Acids
1. In carboxylic acids, the carbon atoms are named in sequence of the Greek
alphabet.
a. The first, excluding the C in the functional group, is named alpha,
and last is omega
b. This applies to amino acids since they have a carboxyl group
i. All 20 naturally-occuring amino acids are alpha-amino acids,
with the amino group attached to the alpha-carbon
2. The alpha carbon is a chiral centre, as it has 4 different groups
a. Except for glycine which has 2 identical groups
b. There are two forms of chiral molecules, dexter (right) or laevus
(left)
i. Determined by CORN rule, COOH, R, NH2 ,H. With the
hydrogen pointed away from the viewer
The L- form has the CO-R-N sequence going counterclockwise
The D- form has the CO-R-N sequence going clockwise
ii. Other naming systems exists, such as R-/S- or d-/lc. L-isomers are the commonly found stereoisomer in nature
i. D-isomers can lead to disease and death
ii. Gramicidin antibiotic contains D-amino acids that perforates
the bacterial membrane
3. Amino acids are amphoteric, due to the amino group being able to accept
a proton, and the carboxyl group being able to donate one.
a. Amino acids always have a charge when in aqueous solution, as
either the amino group, carboxyl group, or both will be charged
i. This is because the loss of charge of one of the groups will
only occur at a pH where the other group is already charged
Check out the pKa to visualise the movement of
protons
ii. Zwitterion occurs when the amino acid has both positive and
negative charge but is electrically neutral
4. There are 20 naturally occurring amino acids, which can be organised into
several groups
a. Non-polar amino acids
i. Alanine, Ala, A
ii. Isoleucine, Ile, I
iii. Leucine, Leu, L
iv. Methionine, Met, M
v. Phenylalanine, Phe, F
vi. Proline, Pro, P
Only amino acid where the R-group covalently links
with the amino group
Affects folding of amino chains
vii. Tryptophan, Trp, W
viii. Valine, Val, V
ix. These are all relatively hydrophobic due to their R-groups, but
still can dissolve in water, with the R-group participating in
hydrophobic interaction
x. Ala, Val, Leu, Ile, Pro are aliphatic. Phe, Trp are aromatic. Met
contains sulphur

xi. They are often found in the protein core, where hydrophobic
interactions causes the protein to fold
xii. The lack of sufficient non-polar amino acids leads to
intrinsically disordered proteins that do not fold into a specific
shape.
b. Acidic amino acids
i. Aspartic acid, Asp, D
ii. Glutamic acid, Gla, E
iii. They contain a carboxyl group that can undergo
deprotonation
iv. At neutral pH, they are negatively charged
c. Basic amino acids
i. Arginine, Arg, R
ii. Histidine, His, H
iii. Lysine, Lys, K
iv. They have an amino group that can undergo protonation
v. Arg and Lys are positively charged at neutral pH, due to the
high pKa of the R-group
vi. Histidine has an aromatic R-group that contains Nitrogen that
can accept a proton
Only the Nitrogen with the double bond can accept a
proton, as it would not disrupt the aromatic ring
structure
d. Polar, uncharged amino acids
i. Serine, Ser, S
ii. Threonine, Thr, T
iii. Tyrosine, Tyr, Y
iv. Asparagine, Asn, N
v. Glutamine, Gln, Q
vi. Cysteine, Cys, C
vii. Ser, Thr, Tyr contain an alcohol group, making them polar.
Asn and Gln are amides, with the NH2 portion unable to
undergo protonation
viii. Threonine has a second chiral centre in its R-group
e. Aromatic amino acids
i. Phenylalanine, Phe, F
ii. Tryptophan, Trp, W
iii. Tyrosine, Tyr, Y
f. Sulfur containing amino acids
i. Methionine, Met, M
ii. Cysteine, Cys, C
iii. Only Cys is able to form disulphide linkages, allowing two
amino acids chains to be linked together.
Disulphide linkages form after the proteins have folded
Helps stabilize the folded structure
g. Glycine, Gly, G
i. Smallest amino acid
Essential for the formation of collagens triple helix as
it is the only one to have a small R-group to fit in the
helixs centre.
5. The pKa of the amino acids are similar
a. The alpha amino group

p ka 9

b. The alpha carboxyl group

c. Acidic side chain (Gla, Asp)
d. Basic side chain (Lys, Arg)

p ka 2
p ka 4
p k a 11 , (His)

p ka 6

6. Amino acids can act as precursors to important molecules

a. Essential amino acids are those the human body cannot produce
and must be found from outside sources (food)
b. Non-essential amino acids are those the human body can produce
7. Amino acids also have an isoelectric point where it is electrically neutral
(zwitterion)
a. Affected by any charges on R-group
b. Located between two pKa
i.

pI =

p K1+ p K 2
, for acidic or uncharged amino acids
2

ii.

pI =

p K2+ p K 3
, for basic amino acids
2

8. Amino acids linked to each other via peptide bonds formed by

condensation reactions
a. The peptide bond is unable to undergo protonation or deprotonation
b. But can still undergo hydrogen bonding
9. Polypeptides are usually named from the N-terminal to the C-terminal
a. The terminals can still undergo protonation and deprotonation
10.There are also non-standard amino acids
a. They can be D-forms of amino acids
b. They can be non-alpha-amino acids
c. They have specific biological functions
d. They arise from posttranslational modification
i. Phosphorylation
Adds PO4H2, that is negatively charged at neutral pH
Can activate or deactivate a protein, acting as a switch

Proteins
1. Proteins are synthesized from mRNA, read in the 5 to 3 direction
a. Produces protein in the N-terminal to C-terminal direction
b. AUG is the start, methionine codon
c. UAA, UGA and UAG are the stop codons that do not code for any
amino acid
2. Proteins are a polymer of amino acids, with a unique sequence of them
a. The primary structures ultimately determines the folding and
function of the protein
b. Proteins are folded into a specific shape, that is not regular
i. There may be local sections that have regular folding, giving
rise to secondary structures
3. There are several ways to determine primary structure of proteins
a. Direct sequencing through protein digestion into fragments, and
then use biochemical methods to determine amino acids present in
fragments
b. Mass spectrometry to determine mass of small protein fragments
and infer amino acids components
c. Prediction from DNA or RNA sequence
4. Protein folding can be visualised by several methods
a. Computational models have various display modes include
wireframe, ball and stick and space-fill
b. X-ray crystallography uses diffraction pattern of X-rays to determine
the three dimensional structure of the protein in a crystal
i. The diffraction patterns is processed to give an electron
density map
ii. The electron density map is used to generate the protein
structure
c. The structure of an unknown protein is likely to be similar to that of
a related known one, and thus can be predicted.
5. The protein needs to be correctly folded to function
a. To allow the binding of specific substrates
b. To catalyse specific reactions
c. For structural proteins to have the mechanical strength, like
collagen
6. Folding is driven by numerous weak interactions, assisted by molecular
chaperones
a. Covalent bonds between amino acids remain unchanged
i. The only covalent bond formed is disulphide linkages after
folding has occurred
Disulphide linkages can be broken by reducing agents
b. Hydrophobic interactions
i. It is the most important factor
c. Hydrogen bonds
i. Give rise to secondary structures
ii. Occurs between peptide linkages and R-groups
d. Ionic bonds
i. Occurs between acidic and basic amino acids
ii. Affected by presence of ions from salts in solution, and pH
e. Van der Waals forces
i. Weaker contributor than the others, but multiple interactions
give rise to a significant effect

7. Denaturing agents like Urea or Guanidinium chloride interferes with

hydrophobic interaction and hydrogen bonds, causing the protein to unfold
8. Under specific conditions, the protein can renature itself, showing that
proteins know how to fold on their own
a. The unfolded protein settles into more energetically favourable
conditions, before settling into the most energetically favourable
configuration
b. Unfolded proteins may aggregate, thus molecular chaperones are
needed inside cell, as they have high protein concentrations
i. Aggregation forms insoluble products that leads to cell death
ii. The molecular chaperones prevent or reverse misfolding
They are hollow to create an environment where the
misfolded protein can fold properly
Example is heat shock proteins that help proteins
refold when under heat stress
9. Secondary structures are local structures in proteins
a. They are held by hydrogen bonds between peptide bonds, and
disulphide linkages
i. There is strong partial charges on CO and NH, due to the
double-bond characteristics caused by resonance structures
The electrons from O can travel to N, creating a full
negative charge on O, and full positive charge on N
Hence, the peptide bond usually has partial
charges for hydrogen bonding
This is due to the shorter than usual C-N bond length
This also prevents free rotation along the C-N bond
Called the amide plane of electron density
along the bond
Thus only the carbon-carbon bond adjacent to
the peptide bond can rotate
Rotation of C -C bond =

(Psi)

Rotation of C -N bond =

(Phi)

b. Regular structures are formed when all the amino acids have the
same Psi and Phi angles
i. Alpha helix
3.6 amino acids per turn
An amino acids has hydrogen bonds with the one 4
residues away
All the CO groups point in the same direction
All the NH groups point in the same, opposite
direction to CO
R-groups extend outwards
All alpha helix are right handed helix, since left handed
helix is impossible due to steric hindrance between Rgroups
Glycine and Proline are rare in alpha helix
Glycine is too flexible and is unlikely to conform
to the same Psi and Phi angles
Proline lacks the NH group to extend the alpha
helix

ii. Beta sheet

Alternating amino acids point in the opposite direction
The Psi bond is the 180 degrees different from
the Phi bond
Thus hydrogen bonds occurs between strands in
the beta sheet
R-groups project above or below the plane of the
beta sheet
Parallel
The C-terminal of each amino acid strand points
in the same direction
Antiparallel
The C-terminal of each amino acid strand points
in different, alternating directions
Proline is rare in beta sheets, as it cannot form
hydrogen bonds and there is a constraint on the Phi
angle
iii. Beta turn
Usually found between antiparallel beta sheets strands
There is an amide plane at right angles to the
plane of the two strands at both ends
Is not a repeating structure like alpha helix or beta
sheet
Commonly contains proline and glycine
iv. Collagen triple helix
10.Super-secondary structures are still local folds, but on a larger scale,
forming motifs
a. They are a combination of alpha helices and beta sheets (with beta
turns), in specific geometric arrangements
i. Beta barrel is found in Green Fluorescent Protein
Made from multiple antiparallel beta sheets, with beta
turns, arranged into a cylinder
ii. TIM-barrel motif is found in Triose Phosphate Isomerase
Made from a sequence of beta, alpha, beta repeating
secondary structures.
b. They are not unique to the protein, and can be repeated within the
protein
11.Another super-secondary structure is domains, which are independently
folded globular units
a. Each domain is like a small globular protein
i. Hydrophobic core and hydrophilic surface
ii. 100 to 200 amino acids long
iii. Has a specific function
iv. Is modular, so can be combined in different combinations for
a different overall protein function
b. Trans-membrane proteins like receptor tyrosine kinases have
domains that allow them to respond to different stimuli
i. The extracellular domains are different to allows binding to
different signalling proteins

ii. The intracellular domains are related, and have a similar

function to act as protein kinases to phosphorylate other
proteins in the cell.
12.Tertiary structure is the global folding of the amino acids into the specific
shape of the protein
13.The evolutionary relationships of species can be determined from their
proteins
a. Homologous proteins have similar amino acid sequences
i. Ortholog is when homologous proteins perform the same
function in related organisms
Arises from a speciation event
This reflects evolutionary relationships as each species
accumulates different mutations when branching from
a common ancestor
ii. Paralog is when homologous proteins within the same
organism has different functions
Arises from a duplication event
Gene duplication eventually results in differing
functions, as evolutions favours the diversity of
additional functions from the copy.
b. Amino acid sequence is not the only indication of relationships
between proteins, structure can show relationships as well
i. Closely related species will have similar sequences and
structures (homology)
ii. Distantly related species can have different sequences, but
similar structures
Their identical protein functions shows that the species
are related
iii. Functionally distinct proteins can also be related, if they have
similar structures
14.Protein types relates to their functions
a. Globular proteins
i. The proteins fold into a compact shape, with a hydrophobic
core, and hydrophilic surface
They are thus soluble in water
ii. They have diverse structures
Thus, have diverse functions
b. Fibrous proteins
i. The proteins largely consists of one type of secondary
structure
It is simple and repeated
Like alpha helices and beta sheets
The hydrophobic residues are in contact with the
environment
Insoluble in water
ii. Thus, they usually have a structural role
iii. Collagen has a triple helix, unique to collagen
3 amino acid chains are wound around each other, with
each chain being a left-handed helix
Has a characteristic amino acid sequences
-(Gly-Xxx-Pro/Hypro)n-

 Only Glycine has an R-group that fits in the core

c. Membrane proteins
i. Integral membrane proteins have a part of the protein within
the membrane, and a part outside
1 or more segments of the protein may span the
membrane
Proteins have a hydrophobic region, and a hydrophilic
one
Around 20 amino acids span the membrane
They are usually in an alpha helix
Polar groups in the peptide bond are
involved in hydrogen bonding
Hydrophobic R-groups face the outside
Receptors and transporters helps to transmit signal or
molecules across the membrane
15.Quaternary structures are formed when multiple proteins are bound
together by disulphide bonds or other non-covalent interactions
a. The protein complex is made up of protein subunits
i. Subunits can be the same type or different types
16.Insulin is needed for the homeostasis of blood glucose levels
a. Is made up of two separate chains linked by disulphide linkages
i. The cell synthesises them together as one long polypeptide
chain, which folds into the correct shape with disulphide
linkages
ii. Protease then cleaves them to produce two linked strands
b. Since the genetic code is the same across all life, E. coli can be used
to synthesise insulin
i. Avoids the problem of immune reaction from using pig insulin
ii. The polypeptide chains are made separately
iii. Denaturing and renaturing processes allow them to fold into
insulin
The instructions for folding is inherent in the protein
17.Prion is an infectious protein, which causes Transmissible spongiform
encephalopathies
a. Prion protein is native to humans, and misfolding causes the
disease phenotype
i. The misfolded PrP is protease insensitive, forming insoluble
fibres, leading to death
ii. Furthermore, the diseased PrP induces normal PrP to misfold
18.Other diseases like Alzheimers may be due to protein misfolding and
aggregation, causing cell death

Enzymes
1. Enzyme is a protein catalyst that increases the velocity of a chemical
reaction, without being consumed during the reaction
a. It has an active site where the substrate can bind for the reaction
catalysis
i. Binding of substrate is held by multiple weak forces
b. They allow for higher reaction rates, as they increase the reaction
velocity
c. They allow for milder reaction conditions, at lower temperatures
d. They allow for greater specificity, as there are no contaminants
produced
i. As in the products are specific, giving high product yields
e. They have a greater capacity for regulation
2. Enzymes fit their substrate either by lock and key model, or induced fit
model
a. In lock and key, the substrate has the exact shape of the active site
b. In induced fit, the binding of the substrate induces a conformational
change in the active site, giving rise to a complementary fit
3. Enzymes require cofactors to function
a. They are non-protein components
i. Inorganic metal ions
ii. Organic molecules (coenzymes)
b. They are like reactants and can get changed, but in the end, they
are regenerated by other processes in the cell
i. Or within the same process for metal ions
c. Prosthetic groups are cofactors that are tightly bound to proteins,
and may be attached covalently.
4. Enzymes are affected by pH
a. pH affects the ionization of R-groups in the protein amino acids
i. This changes substrate-active site interaction, affecting
enzyme activity
5. Enzymes are affected by temperatures
a. The enzyme activity decreases at extreme temperatures due to
denaturation
i. Else the rate of reaction would have increased linearly, like in
a non-enzyme catalysed reaction
6. Reactants converting to products go through a transition state
a. It is their highest level of free energy
i. It is highly unstable and cannot be extracted
b. Activation energy is the energy required to get them to the
transition state
i.

= activation energy. is double dagger

7. Unlike Chemistry, even though

K >1, G <0 , the reaction may not be

spontaneous, due to high activation energy

a. The reaction is thermodynamically feasible, but may not be
kinetically feasible
8. Enzymes lower the activation energy of the reaction, without affecting
other thing like K or

a. They accelerate both the forward and reverse reactions, so

equilibrium is not affected

9. The enzymes are complementary to the reactions transition state

a. If it was complementary to the reactants, the bonded state would
be energetically lower than the transition state, thereby further
increasing the activation energy
b. Both the enzyme and substrate interact to reach the transition
state, thus lowering the energy needed
10.Enzyme catalyse reactions by 3 ways
a. Acid-base catalysis
i. The enzyme adds or accepts a proton from the functional
group of the substrate, making it more reactive
It helps create the partial charges formed in the
transition state
ii. The acidic and basic amino acids can do this, as they are
have R-groups that are either in native or conjugate acid/base
state.
iii. The protons accepted or donated are regenerated by water
b. Covalent catalysis
i. There is a transient formation of an enzyme-substrate
covalent bond
ii. Due to nucleophilic attack of enzyme nucleophile to
electrophile substrate
The electron rich atom is usually O, S or N, and can
bond with electron deficient atoms like C, protons or
metal ions
iii. The covalent bond pulls electrons away from the reaction
centre, allowing the other part of the substrate to be attacked
c. Metal ion catalysis, with the ion from the environment
i. The metal ions bind to both the substrate and enzyme,
orientating the substrate
ii. The metal ion stabilize negative charges during transition
state
The positive charges help reduce repulsion between a
negative group and electron pairs on attaching
nucleophiles.
iii. The metal ion can promote nucleophilic attack, by allowing
the electrons to be passed along a chain of water
The water gets ionized while passing the charge to the
metal ion
The hydrogen bond network, a series of formation and
breaking of hydrogen bonds as the electrons are
passed.
iv. Metal ions also allow for carbonic anhydrase
The metal ion accepts a OH- ion produced from water
The OH- ion attacks nearby bound substrate CO2 to
form HCO3 The catalytic site is then regenerated by another water
molecule

Kinetics
1. The step with the higher activation energy, is the slowest step. Thus it is
the rate-determining step
a. Unlike the transition state, the intermediate product between
reaction steps can be extracted
2. The velocity of the reaction is the change in concentration of reactant or
product per unit time
a. Velocity unit is M per second.
i. Short essay question answers needs to contain units

d [P] d [R ]
=
, where R is reactant, and P is product
dt
dt

b.

v=

c.

v =k [ R] , where k is the rate constant

3. The order of the reaction depends on the number of molecules

participating in the rate-determining step
a. First-order reaction has only one molecule, second-order has two.
i. The two molecules can either be the same or different
b. The rate equation changes depending on the order of reaction
c. Third-order is rare, as simultaneous collision of three molecules is
rare
4. While chemical reaction rates can continue to increase indefinitely with
increasing concentration, enzyme-catalysed reactions have a plateau
a. At low substrate concentration, velocity is linearly proportional to it
b. As substrate concentration increase, the velocity approaches its
maximum, causing the rate of increase to be less than linear
c. At high substrate concentrations, the velocity is independent of
substrate concentration
i. Other factors still affect velocity, like temperature, pH and
enzyme concentration
5. Michaelis-Menten Equation:

V 0=

V max [ S]
K M +[S ]

a. At the initial reaction velocity, there is no reverse reaction of

product becoming substrates, and the concentration of enzymesubstrate complex is constant
i. The rate of formation of the ES complex is equal to its
dissociation rate
b.

KM

is the Michaelis constant:

KM=

k1+ k 2
k1

i. It is equal to the rate constant of the breakdown of ES

(forward to form products, and backwards to substrate),
divided by the rate constant of the formation of ES
1

ii. Unit is
c.

V max

1 1

M s

=M

is the maximum velocity, and occurs at high substrate

concentration where all the enzymes are in enzyme-substrate

complexes.

6.

KM

is also the initial substrate concentration when the initial reaction

velocity is half its maximum

a. This is derived from the Michaelis-Menten equation
b. The equation also shows how the reaction is zero-order at high
substrate concentration, and first-order at low substrate
concentration
c. The smaller the

KM

value of the enzyme, the lower the substrate

concentration needed to achieve maximal velocity

i. It is unique for each enzyme-substrate pair
ii. It is a measure of enzyme affinity for the substrate

KM

1
affinity

7. The disadvantage to the Michaelis-Menten plot is the difficulty in finding

V max

and

K M , as large substrate concentrations are needed for the

curve to plateau.

V max

a. Even then,

might not be obvious

8. The alternative is to draw the Lineweaver-Burk plot, that is a doublereciprocal plot

a.

1
v

is plotted against

1
[S ]

KM 1
1
1
=
+
V 0 V max [ S ] V max

( )

i.

b. The y-intercept is

V max , as the substrate concentration

approaches infinity
c. The x-intercept is

1
KM

i. It is negative, as it is found behind the y-axis, since there is

no natural way for the velocity to increase above

V max

ii. It is derived from the equation

d. The gradient of the slope is
9.

k cat

KM
V max

is the turnover number, the number of substrate molecules

converted to product per enzyme molecule, per unit time, when the
enzyme is saturated with substrate
a.

V 0=k cat [ ES]

b.

V max =k cat [ E ]total

c.

k cat =k 2

10.Catalytic efficiency:

k cat
KM

a. It is the efficiency of the enzyme at low substrate concentrations

b.

V0

k cat
[ E ] [S]
K M total

11.Irreversible inhibition is when the inhibitor forms covalent bonds with the
functional groups at the active site of the enzyme
a.

V max

b.

KM

decreases, as effective enzyme concentration decreases

KM

decreases, with the

decreasing proportionally to

V max
12.Reversible inhibition is when the inhibitor associates reversibly with the
enzyme at various sites
a. Competitive inhibitors binds to free enzyme at the active site,
competing with substrate binding
i. They are structural analogues of the substrate

KM

ii. They increase the

of the enzyme without affecting

V max
iii.

V 0=

V max [S ]
K M +[ S] , where
KI

=1+

[I ]
KI

is the dissociation constant for the formation of

EI from E and I

KI =

k3
k3

iv. The effects of the competitive inhibitor can be reduced by

increasing substrate concentration
b. Uncompetitive inhibitors only bind to the enzyme-substrate complex
i. This affects the enzyme conformation, reducing the catalytic
capacity
ii.

V max

and

KM

proportionally to

decreases, with the

decreasing

V max

The, enzyme is unable to catalyse the reaction as

effectively, decreasing

KM

KM

V max

decrease as well, as

k2

is equal to

V max

proportionally

k2

is reduced

at high substrate

concentration, thus the decrease is proportional

iii.

V max

) [S]
'

V 0=
, where
K
( M' )+[ S ]

K 'I

' =1+

[I ]
K 'I

is the dissociation constant for the formation of

ESI from ES and I

iv. The substrate binding to free enzyme is unaffected
c. Non-competitive/ mixed inhibitors bind to both the free enzyme and
enzyme-substrate complex
i. The

V max , will definitely decrease, as ESI affects catalytic

activity

KM

ii. Change in
ES

depends on affinity of inhibitor with E and

If

KI

is greater, then

KM

will increase

If

'
I

is greater, then

KM

will decrease

If they are equal, there will be no change in

Pure non-competitor

)[ S]
'
V 0=
K M
( ' )+[S ]

iii.

V max

KM

Enzyme regulation
1. Enzyme activity is dependent on their concentration and affinity for the
substrate
a. By changing the rate of transcription, translation and degradation,
enzyme activity can be controlled
b. There are also modifications that can be done to the enzyme to
regulate their activity
2. Glucose levels in the cell are controlled by hexokinases I to IV, which
phosphorylate the glucose to prevent their transport out of the cell.
a. Hexokinase I to III are found in most tissues except liver
i. They have a low

KM

, that allows for utilisation of glucose

when blood glucose is low, by trapping the glucose in the cell

ii. Their

V max

is low as well, excessive levels of glucose is not

needed
b. Hexokinase IV (glucokinase) is found in the liver cells
i. They have a high

V max

to allow the uptake of large

amounts of glucose from the blood

ii. They also have a high

KM

to allow for the phosphorylation

to occur mainly at high blood glucose concentrations

iii. This buffers the level of blood glucose, by removing excess
glucose and storing them in the liver.
3. Enzyme activity can be regulated by localization, by isolating the enzyme
from the substrate
a. Glucokinase activity in liver cells is regulated by Glucokinase
regulatory protein (GKRP)
b. GKRP will competitive inhibit the binding of glucose to hexokinase IV
i. Once bound, GKRP inactivates glucokinase by bringing it into
the nucleus
c. Thus formation of more GKRP-GK complexes reduces enzyme
activity
i. GKRPs affinity for GK is increased in the presence of Fructose
6-phosphate, another sugar source
ii. Whereas, higher levels of glucose reduces the overall activity
of GKRP
iii. Thus, at low blood glucose levels, Hexokinase IV activity is
reduced as it is bound to GKRP
Prevents the liver from competing with other organs for
glucose
d. Overall, glucokinase activity is regulated by three factors
i. Its own kinetics property

High

KM

ii. Binding to GKRP that inactivates it

iii. The level of expression of glucokinase gene
In response to insulin levels, as insulin induces more
glucokinase production to reduce blood glucose levels
4. Enzyme activity is also regulated by cleavage activation
a. Some enzyme are synthesized in their proenzyme (zymogen) form
i. These are inactivated and require cleavage to be activated

ii. Like proteolytic enzymes of digestive tract and blood clotting

proteins
iii. They have either Pro- as prefix, or ogen as suffix
b. Autocatalysis may occur to speed up activation at desired site
i. Where the product acts as a cofactor to the cleaving enzyme
Enteropeptidase requires trypsin to cleave trypsinogen
into trypsin
c. Self-digestion can also occur to further cleave excess amino acids
i. Chymotrypsinogen is partially activated through trypsin
cleavage to give pi-chymotrypsin
ii. Pi-chymotrypsin will self-digest to produce alphachyymotrypsin that is fully activated
d. For proteases, trypsin, once activated, will cleave several other
proenzymes to activate them
i. Thus this is like a cascade of enzyme activation
e. Enzyme activation can occur through different stimulus
i. Blood clotting is triggered by either external damage to tissue
surface, or internal trauma
ii. Both start different cascade reactions that eventually produce
Factor Xa
iii. Factor Xa cleaves prothrombin into thrombin, allowing it to
cleave fibrinogen into fibrin
iv. Fibrin then aggregates into the clot
5. Enzyme activity is regulated by allosteric regulation
a. Through the non-covalent binding of effectors at a regulatory site
other than the active site
b. Protein usually consists of multiple subunits, and the binding of
effectors changes their conformation
i. Negative effectors inhibit enzyme activity
ii. Positive effectors promote enzyme activity
iii. When conformation changes, the shape of the active site
changes, affecting its affinity to the substrate.
c. Homotropic effectors are the substrates that bind to the regulatory
site to affect the binding of substrate to the active site
d. Heterotropic effectors are effectors other than the substrate
e. When allosteric enzymes have multiple active site, each active site
acts as a regulatory site for other active sites
i. Thus the binding of one substrate will influence the binding of
substrate to the other active site (Cooperative substrate
binding)
Cooperativity can be positive or negative
A sigmoid curve (S shape) results when active site
affinity keeps switching depending on number of
substrates already bound
f. This allows for feedback inhibition, where the high concentration of
products will reduce enzyme activity, by binding to it as a negative
effector
i. Need not be product directly, as it can undergo further
modification before becoming the negative effector
g. Other enzymes can be in the inactive state until the required
cofactor (positive effector) binds to the regulatory sites to expose
the active sites.

i. The catalytic subunits can also detach or rejoin the regulatory

subunits depending on presence of cofactors
6. Lastly, enzyme activity can be regulated by covalent modification of the
enzyme
a. Modifications include
i. Phosphorylation
Adding of phosphate group
ii. Methylation
Adding of methyl group
iii. Uridylylation
Adding of uridine base
iv. Adenylylation
Adding of adenine base
b. Phosphorylation of glycogen phosphorylase causes a conformational
change into a more active state
i. This increases the rate of phosphorylation of glycogen, which
extracts a glucose 1-phosphate from the glycogen chain of
glucose
7. Enzyme can be regulated by a combination of the above methods
a. Glycogen phosphorylase can be activated by phosphorylation
(covalent modification) or binding of effectors (allosteric regulation)
i. Positive effector is AMP
ii. Negative effector is ATP and glucose-6-phosphate
Haemoglobin and Myoglobin
1. Heme is a complex of an organic molecule (protoporphyrin IX) and ferrous
iron (Fe2+)
a. The iron is held in the centre space of the molecule by four
Nitrogen atoms in the porphyrin ring
b. The iron has six liganding positions, of which the 4 liganding
positions that lie on the same plane are taken up by protoporhyrin
IX
i. Thus 2 more liganding positions, above and below the plane,
are available for bonding to other ligands
In myoglobin, one of the protein domains is the fifth
ligand, allowing oxygen to bind to the 6th and last slot.
2. Myoglobin is an oxygen binding protein that comes in different forms
a. Deoxymyoglobin contains ferrous iron (Fe2+) in the heme group, but
the 6th ligand position is vacant and available for binding to oxygen
b. Oxymyoglobin contains ferrous iron (Fe 2+) in the heme group, with
the 6th ligand position occupied by oxygen
c. Metmyoglobin contains ferric iron (Fe 3+) in the hematin group, with
the 6th ligand occupied by water
i. Due to the oxidation of the iron, the heme turns into hematin,
preventing binding to oxygen
ii. The metmyoglobin thus cannot function as an oxygen
transport protein
3. The globin component helps to protect and control the heme group
a. Heme can bind to oxygen by itself, but it can also freely bind to
carbon monoxide with a higher affinity
b. The globin group cradles the heme group, protecting the iron ion
from further oxidation

4.

5.

6.

7.

c. The globin group also decreases the affinity of heme for carbon
monoxide
i. This is done by steric hindrance, where the amino acid
residues near the 6th ligand position forces carbon monoxide
from its preferred perpendicular alignment
The carbon monoxide has to bend at a 120 degrees
angle instead, thereby making it less likely to bind
Its affinity decreases from 25000 times that of oxygen,
to 250 times
The binding of oxygen to the iron ion in heme drags it towards the oxygen
molecule.
a. This then pulls on the amino acid residue in the globin chain,
leading to a conformational change
Hemoglobin consist of 4 myoglobin subunits (tetramer), two alpha chains,
and two beta chains
a. Each alpha chain is in contact with two beta chains, and vice versa
i. Little alpha-alpha chain interaction and vice versa
ii. A alpha chain interacts with one of its beta chain neighbours,
forming 2 alpha-beta dimers altogether
Strong hydrophobic interactions between the two
chains in the dimer
Weak hydrogen and ionic bonds between the two
dimers
b. Each subunit has a heme group that can bind to oxygen
i. Thus each hemoglobin molecule can bind 4 oxygen molecules
c. When one myoglobin subunit binds to an oxygen molecule, the
conformational change affects its interaction with the other subunits
i. The change in quaternary structure weakens the bonds
between the two alpha-beta dimers
The hemoglobin changes from the deoxy form (T state)
to its oxy form (R state)
ii. In the T conformation, oxygen can only bind to the accessible
heme groups in the alpha chains
Steric hindrance prevents binding to the beta chainss
heme
iii. Thus there is cooperative binding of oxygen, as transiting to
the R conformation allows binding to the heme groups in the
beta chains
Hemoglobin and myoglobin have different properties (affinity for oxygen)
a. Hemoglobin has a steep oxygen dissociation curve at the oxygen
concentrations occurring in tissues.
i. Thus oxygen can be released when hemoglobin reaches the
tissues
ii. This steepness also allows it to respond to small changes in
tissue oxygen pressure, releasing more or less oxygen when
needed
Hemoglobins affinity for oxygen is affected by pH
a. The Bohr effect, where greater acidity (lower pH) leads to lower
affinity for oxygen
i. Greater oxygen pressure is needed for saturation, and less
oxygen is transported to the tissues

ii. However, more of the oxygen in hameglobin is released due

to the lower affinity, as less oxyhemoglobin leaves the tissues
b. The binding of protons (H+) to the hemoglobin promotes the
dissociation of oxygen, thus reducing affinity for oxygen binding
i. The protons will induce the hemoglobin into the T form,
hindering binding of oxygen
By promoting ionic bonding between amine and
carboxylic acid
Carboxylic acid is usually negatively charged as the pH
does not fall to low levels enough for it to protonate
Thus lower pH will cause the amino group to protonate
8. Hemoglobins affinity for oxygen is also affected by carbon dioxide
a. Carbon dioxide dissolved in the blood reacts with the water to give
carbonic acid
i. This reduces the blood pH, as protons are produced from the
dissociation
b. Carbon dioxide can also react with the N-terminal of the subunits in
hemoglobin, producing carbamate that forms salt bridges which
stabilise the T conformation
i. This also produces protons that further decrease the pH
c. Thus the higher carbon dioxide concentration near the tissues
promote the release of oxygen from the hemoglobin due to the two
effects that favour the T conformation
9. Lastly, Hemoglobins affinity for oxygen is affected by 2,3Bisphosphoglycerate (BPG)
a. 2,3-BPG is an abundant organic phosphate in red blood cells
b. 2,3-BPG binds to the positively charged cavity only present in
deoxyhemoglobin
i. The cavity is formed by the two beta chains, and is positively
charged due to the amino acid residues facing the cavity
ii. This reduces hemoglobins affinity for oxygen, as the T
conformation is stabilised
The oxygen dissociation curve is shifted to the right,
meaning more oxygen is released at the tissues
Needed for high altitude environments
c. Fetal hemoglobin contains a different subunit (gamma) that has a
lower affinity for 2,3-BPG
i. This increases its affinity for oxygen
ii. It binds to oxygen released by the maternal hemoglobin,
allowing for the fetal tissues to be supplied with oxygen
10.Sickle Cell Anemia is caused by a mutation in the gene coding for
hemoglobin
a. This results in a protrusion in the beta-chain subunit
i. The protrusion can fit in hydrophobic pocket present only in
deoxyhemoglobin
ii. This causes the polymerisation of HbS, forming insoluble
fibers when oxygen is released
b. The formation of fibers deforms the red blood cell, hindering its
movement through tiny blood capillaries, reducing blood flow,
preventing efficient oxygen transport
Nucleic Acids

1. Chargaffs rule states that the amount of purines equals the amount of
pyrimidines in DNA
a. Purines are Adenine and Guanine
b. Pyrimidines are Thymine, Cytosine and Uracil
c. Later explained by complementary base pairing
2. 3-5 phosphodiester bonds joins the nucleotides together
3. Beta-glycosidic bonds join the nitrogenous base to the carbon ring
4. DNA double helix structure results in a major groove and a minor groove
a. Major groove where the vertical distance between a backbone and
the next one is bigger
i. Due to the angle of the glycosidic bonds between the carbon
ring and nitrogenous base
b. Minor groove where the vertical distance is lesser
5. DNA has three conformations
a. B-DNA is commonly found
i. It is right handed
ii. Its major groove is wide with medium depth
iii. Its minor groove is narrow with medium depth
b. A-DNA is synthesized in the lab, when DNA is dehydrated
i. It is right handed
ii. Its major groove is narrow but deep
Still called major groove as it is the analogous location
in B-DNA
iii. Its minor groove is broad but shallow
c. Z-DNA occurs when there are CpG repeats (p stand for phosphate)
i. It is left handed
Due to glycosidic bonds for pyrimidines being in the
syn-position
All glycosidic bonds are in the anti-position in A
and B-DNA
Can be transitioned to from B-DNA, by the rotation of
those bonds
May be linked to regulation of gene expression
Methylation of cytosine promotes this transition
ii. Its major groove is flattened out
iii. Its minor groove is narrow but deep
6. In prokaryotes, their closed loop DNA can undergo supercoiling
a. It is usually negatively supercoiled
i. Against the direction of DNA rotation
b. The topology of supercoiling is determined by the Link number
i. Link number = number of twists + number of writhing
Twists is the turning about the helical axis
Can be positive or negative
Related to tension
Writhing is the number of turns around the superhelical
axis
Can be positive or negative
Related to supercoiling
Any combination of Twists and Writhing is possible so
long as they equal the link number
ii. Link number can only be changed by topoisomerase that cut
the strand

7. In eukaryotes, DNA is compacted into chromatin

a. DNA is coiled around histone proteins to form nucleosomes
i. Histone have many arginine and lysine residues that are
positive charged to bind to the negatively charged
phosphates in the DNA backbone
b. Nucleosomes compact to form solenoid, which compacts to form
loops, which compact to form metaphase chromosome
i. Chromosomes have dark and light banding when stained
GC rich regions are light bands that usually contain
more genes
AT rich regions are dark bands that usually contain less
genes
ii. The location on a chromosome can be written in the format
AA q/p BB
Where AA is the chromosome number
q or p refers to the shorter or longer arm
Where BB is the region and band
Number is counted from the centromere and
may not start from 1
8. Karyotypes are written in the format AA,XX
a. Where AA is the total number of chromosomes
b. Where XX are the sex chromosomes
9. RNA is usually single stranded, but can form secondary and tertiary
structures
a. Not all bases needs to be complementary paired, thus giving a
budge that is the secondary structure
i. The junction secondary structure of tRNA allows for base
pairs to stick out of the molecule, to interact with the codons
on mRNA
The arms of the junction structure interact with each
other, giving rise to a tertiary structure
ii. The base pairs can either stick out externally or internally,
thereby giving a bulge
b. mRNA can interact with metabolites, causing a change in
conformation, which can restrict access to the translation initiation
site
c. Double-stranded RNA can also control gene expression through RNA
interference
i. Dicer (a protein) cleaves dsRNA to produce siRNA (small
interfering)
siRNA, also known as silencing RNA, is still double
stranded
ii. RNA-induced silencing complex (RISC) binds to siRNA and
separates it
RISC-siRNA complex uses the siRNA as a template to
bind to mRNA and cleave it to disrupt gene expression
10.DNA replication occurs in the 5 to 3 direction, with DNA polymerase
adding nucleotides to the 3 end of an existing strand
a. The existing 3 OH group carries out a nucleophilic attack on the
phosphate group of the incoming nucleotide

b. DNA polymerase also has exonuclease activity that can remove

bases
i. 3 to 5 exonuclease is used for proofreading, for the excision
of mismatched bases
The proofreading ability of DNA polymerase III in
prokaryotes
ii. 5 to 3 exonuclease is used for replacement of bases, from
the nick onwards
Such as the replacement of the RNA primer by DNA
polymerase I in prokaryotes
11.DNA replication in prokaryotes
a. Initiation occurs at the origin of replication (oriC)
i. DnaA binds to the oriC, which is AT rich
ii. DnaA recruits DnaB which acts as helicase to unwind the DNA
iii. DNA gryase helps to prevent supercoiling as the DNA unwinds
iv. Single strand binding proteins help to prevent single strands
from reanneling
b. DNA polymerase III holoenzymes consists of several subunits
i. Alpha, epsilon and theta subunits synthesizes DNA in the 5
to 3 direction
ii. Beta subunit functions as a clamp to keep the complex
associated with DNA
This increases the polymerisation rate by preventing
dissociation
iii. Other subunits are the clamp loader complex that loads the
clamp onto the DNA periodically every 1000 nucleotides onto
the lagging strand
c. Primase adds the RNA primer on the lagging strand
d. DNA polymerase I replaces the RNA with DNA, using a 5 to 3
exonuclease
i. It also has proofreading abilities.
e. DNA ligase seals the nick between nucleotides, joining the Okazaki
fragments together to from a continuous daughter strand
i. The replacement of the last nucleotide of the RNA primer
does not automatically join it to the next fragment
12.DNA replication in eukaryotes
a. Eukaryotes have several oriC
b. Origin recognition complex (ORC) binds to the origin of replication to
prepare the strands for replication
i. During the G1 phase, ORC recruits replication activator
protein (RAP) to bind to itself
ii. RAP recruits replication licensing factors that bind along the
DNA molecule
iii. This pre-replication complex (ORC/RAP/RLF) primes the DNA
for replication
c. During S phase, cyclin-dependent kinases (CDKs) phosphorylate the
complex to activate DNA replication by recruiting DNA polymerase
and primase
i. This phosphorylation also degrades the RAP and RLF to
prevent formation of another pre-replication complex,
preventing further DNA replication

ii. Polymerase delta synthesises the daughter strand on both

the leading and lagging strands
iii. Polymerase alpha is associated with primase for DNA
replication on the lagging strand
This DNA polymerase cannot proofread
Replicates DNA only on the lagging strand for a length
of base pairs, before polymerase delta replaces it and
continues synthesis
Before polymerase delta can reach the RNA primer of
the next fragment, FEN-I nicks the RNA primer,
allowing RNase-H1 to remove it
Polymerase delta then replicates to the DNA portion of
the next Okazaki fragment, with DNA ligase sealing the
nick to join the fragments
iv. Both DNA polymerases are help in place by proliferating cell
nuclear antigen (PCNA)
PCNA is loaded by replication factor C
d. Replication proteins (RPA) help stabilize the single strands during
replication
e. Telomerase can overcome the 3 end replication problem, by
lengthening the telomeres
i. This prevents cellular senescence
ii. Telomerase is a ribonucleoprotein
Its RNA component is complementary to the telomeric
repeats
Telomeres have tandem repeats of G-rich
regions
The RNA binds with a portion exceeding the
telomere
The catalytic subunit telomerase reverse transcriptase
(TERT) extends the 3 end of the leading strand using
the RNA template that is not bound to the DNA
The lagging strand is then extended by the same DNA
replication machinery
13.DNA in an organism can be shuffled around by recombination processes
a. Homologous recombination occurs during meiosis or during repair of
double stranded breaks
i. Crossing over and exchange of DNA occurs between
homologous sequences
ii. There is a formation and resolution of a Holliday junction
RecBCD contains helicases that unwinds both strands
of DNA, producing a 3 invading end
RecBCD consists of three subunits, Rec B, Rec C
and RecD
RecA binds to the 3 invading strand and helps direct
strand invasion
It binds to both the single stranded 3 invading
strand, and the homologous double stranded
DNA
It travels along the homologous chromosome
until it finds the complementary region

 The invading strand displaces the

complementary strand in the homologous
chromosome
DNA ligase then joins the invading strand with
the invaded strand
Branch migration then occurs where the holiday
junction moves further away from the point of invasion,
causing more DNA to be swapped between the two
homologous chromosomes
RuvABC complex (has three subunits) has
helicases in RuvA and RuvB to unwind each
homologous chromosome, allowing the branch
to migrate
Resolution of the holiday junction occurs when the DNA
twists to form a 4-way junction
RuvC resolvase then cleaves the holiday junction
either vertically or horizontally
The alleles downstream of the junction may or
may not be exchanged depending on the
cleavage
b. Transposons are mobile genetic elements that can change their
position within the genome
i. Class I are retrotransposons that proliferate by a copy and
paste method
The RNA of the transposon is synthesised
Reverse transcription occurs to produce a DNA
molecule complementary to the RNA
The reverse transcriptase may be encoded for
by the transposon
The DNA molecules then invades the DNA chromosome
at another location away from the original transposon
This increases the number of transposons in the
chromosome
ii. Class II are DNA transposons that move about by cut and
paste method
The transposon is flanked by repeating sequences that
contain a recognition sequence
It is cut and extracted from the DNA chromosome by
transposase that produce blunt ends
Transposase is encoded for by the transposon
Another location along the DNA that contains the
recognition sequence is cut by enzymes that produce
sticky ends
May be specific or non-specific depending on the
transposase, so long as they contain the
recognition sequence
The transposon is then inserted into this position
The gaps from the sticky ends are then filled in by DNA
polymerase and ligated by DNA ligase

The number of transposons stay constant and only

move about
14.DNA mutation occurs due to errors or mutagens
a. Spontaneous errors can occur during DNA replication through
substitution, insertion, deletion, depurination or deamination
i. Substitution can either be transitions or transversions
Transitions causes a purine to be substituted by the
other purine, and a pyrimidine by another pyrimidine
Transversion causes a purine to be substituted by
either pyrimidine and vice-versa
These wobble base pairing is non-Watson-Crick paring
If not corrected, it is incorporated into the
daughter strand after DNA replication
The wild type strand produces a wild type
daughter strand, while the mutant strand
produces a mutant daughter strand that does
not experience wobble base pairing
ii. Depurination results in a loss of a G nitrogenous base
If not repaired, the damaged strand will always
produce a mutant daughter strand with a random
nucleotide at the damaged position
This leads to several types of mutant
chromosomes that continue to proliferate since
the damaged strand produces a different mutant
daughter strand with different nucleotide used
as the damaged location
iii. Deamination removes an amine group from the nitrogenous
base
A cytosine base is converted to a uracil
A methylated cytosine base is converted to a thymine
b. Mutagens are UV radiation, HNO2, ionisation radiation and alkylating
compounds
i. UV radiation causes the formation of pyrimidine dimers
ii. HNO2 causes deamination
iii. Ionisation radiation and alkylating compounds causes
chemical modification of bases
15.DNA repair mechanisms correct the mutations by removing the damage
a. Base excision repair (BER) places a single damaged base
i. The damaged nitrogenous base is removed by DNA
glycosylase that breaks the glycosidic bond, forming an
Apurinic/apyrimidinic (AP) site
ii. AP endonuclease then creates a nick to remove the sugar
ring and phosphate group of the damaged nucleotide
iii. The gap is then repaired by DNA polymerase that adds the
correct nucleotide
iv. DNA ligase seals the nick between the new nucleotide and
the sugar phosphate backbone downstream.
b. Nucleotide excision repair (NER) replaces a section of DNA, usually
for bulky lesions like pyrimidine dimers
i. NER complex binds to the damaged section and the area
around it

It separates the two strands which are stabilized by

proteins
Single strand binding proteins for prokaryotes
RPA for eukaryotes
It then cleaves the ends at either side of the damaged
DNA, removing a section of the DNA strand
Then recruits DNA polymerase and DNA ligase to use
the remaining strand as a template for repair and
ligation
c. Mismatch repair (MMR) corrects incorrectly paired bases that were
missed during DNA replication
i. The template parent strand is identifiable since it is
methylated
ii. MutS binds to the mismatched base and recruits MutL and
MutH
MutH binds to the DNA molecule at a hemimethylated
site away from the damage and is connected to MutS
through MutL
Hemimethylated since only the parent strand is
methylated
iii. MutH then nicks the unmethylated daughter strand
iv. An exonuclease then degrades the DNA from the MutH nick
until the mismatched base on the daughter strand
Different exonuclease is recruited depending on
whether the nick is a 3 or 5
v. DNA polymerase then fills in the gap and DNA ligase seals the
nick
d. Non-homologous recombination repairs a double stranded break
without a use of a template, resulting in error-prone repair.
i. The double-stranded break recruits Ku70/Ku80 proteins (a
heterodimer)
ii. The Ku proteins recruits accessory proteins
Artemis:DNA-PK nucelease complex resects the
damaged DNA ends
It a complex consisting of the artemis protein
with DNA-dependent protein kinases
DNA polymerase fills in the gaps
DNA ligase ligates the ends
e. Homologous recombination repair uses the undamaged homologous
copy as a template for repair
i. It can only occur when there is a homologous chromosome
present after S phase
ii. ATM kinase detects the double stranded break and recruits
the MRN complex
MRN complex consists of Mre11, Rad50 and Nbs1
iii. Rad52 is then recruited to process the ends to form 3 single
stranded ends
iv. BRCA2 recruits Rad51 which binds to the single strands to
promote strand invasion
Rad51 is homologous to RecA in prokaryotes

v. Rad54 helps Rad51 to find the homologous region during

strand invasion
vi. DNA polymerase fills in the gaps and DNA ligase fills the nicks
vii. Resolvase resolves the Holliday junction
Lipids
1. Lipids are organic molecules that have certain characteristics and
functions
a. Characteristics
i. Low solubility in water
ii. High solubility in nonpolar solvents
iii. Mostly hydrocarbon in nature
b. Functions
i. Energy storage
ii. Cellular membranes
iii. Biological signals
2. Lipids are made from fatty acids with hydrocarbon chains that terminate
with a carboxyl group
a. They have an even number of carbons between 14 and 24
b. The hydrocarbon chains can be either saturated or unsaturated
i. Cis double bonds introduces kinks in the hydrocarbon tail,
preventing close packing that lowers the melting point
c. Named in the manner x:y n-z
i. Where x is the number of carbon, and y is the number of
double bonds
ii. If the fatty acid is unsaturated, z is carbon number that
contains the first double bond when counted from the methyl
end
Note that when naming, the first carbon is the one in
the carboxyl group
3. Triacylglycerols are formed from the esterification between three fatty acid
molecules and one glycerol molecule
a. A simple triacylglycerol consists of three of the same fatty acids,
while in mixed triacylglycerol they are different
b. It functions as an energy storage compound, in adipose tissue
i. It is broken down by lipases through hydrolysis to produce
energy
ii. It can react with NaOH to form soap through saponification
The strong base causes base catalysed hydrolysis
c. It is not found in lipid membranes
4. Glycerolphospholipids consists of a glycerol-3-phosphate with two fatty
acid chains
a. The hydrophobic fatty acid tails and polar phosphoryl group makes
it a good component for lipid membranes as it is amphipathic
b. The phosphoryl group can also be bonded to another group, giving
rise to different forms of glycerolphospholipids
i. Phosphatidic acid (PA): -H
ii. Phosphatidylethanolamine (PE): -CH2CH2NH3+
iii. Phosphatidylcholine (PC): -CH2CH2N(CH3)3+
iv. Phosphatidylserine (PS): -CH2CH(NH3+)COOv. Phosphatidylinositol (PI): ionositol (a 6 carbon ring)
Can be phosphorylated to form signalling molecules

vi. Phosphatidylglycerol (PG): -CH2CH(OH)CH2OH

Diphosphatidylglycerol can be formed by another
glycophospholipid bonding with the substituent
glycerol
c. When hydrolysed by phospholipases, signalling molecules are
formed
i. Phospholipase A2 can produce arachidonic acid that is a
precursor for prostaglandins, leukotrienes and thromboxanes
Prostaglandins are cyclic fatty acids that have
hormone-like effects like promotion of uterine
contractions
Leukotrienes are produced by leukocytes and regulate
immune responses by acting as inflammatory
mediators
Thromboxanes is involved in clot formation as a
vasoconstrictor
5. Sphingolipids are derivatives of sphingosine
a. Sphingosine is a 18-carbon amino alcohol, and the amino group
forms an amide bond with a fatty acid molecule
i. This gives rise to ceramide, a parent compound for
sphingolipids
b. Different groups can react with the alcohol group on ceramides
i. Sphingomyelin are formed with phosphocholine or
phosphoethanolamine
Differs from phosphatidylcholine and
phosphatidylethanolamine
It is the choline group with a phosphoryl group, without
the glycerol or fatty acids
ii. Cerebrosides are formed with simple sugars
iii. Gangliosides are formed with complex sugars with at least
one sialic acid bonded to any residue of the sugar
c. Sphingomyelin is the most common sphingolipid, forming 10% to
20% of the lipid membranes
d. Gangliosides are found on the cell surface of lipid membranes and
serve as receptors
i. The oligosaccharide bind to ligands
Ligands like toxins or viruses
ii. Fatty acyl chains anchors the ganglioside to the lipid
membrane
6. Terpenes are a diverse group of lipids derived from 2 or more units of
isoprene molecules
a. Isoprene is a five carbon molecules that can polymerase repeatedly
due to it having two carbon bonds
b. Monoterpenes are made from two isoprene molecules
i. Found in plants
ii. A component for flavour or odor
c. Diterpenes are made from four isoprene molecules
d. Triterpenes are made from six isoprene molecules
i. Squalene is a triterpene that is a precursor to steroids
7. Steroids are derivatives of cyclopentanoperhydrophenanthrene that is built
from isoprene

a. The most common steroid is cholesterol which is also a precursor for

other steroids
i. Like hormones or bile acids
b. Cholesterol is a constituent of plasma membranes
i. It buffers the fluidity of the cell membrane
At cellular temperatures, it decrease fluidity by
stabilising the extended conformation of the
hydrocarbon tails of fatty acids with its fused ring
structure
At lower temperatures, it increases fluidity by
preventing the close packing of the lipids as it
separates the groups
8. Cellular membranes are made from lipid bilayers
a. The amphipathic lipids will form spontaneous structures in water
i. Either a monolayer micelle
ii. Or bilayer vesicle
A cell membrane is a very large vesicle
b. Lipid bilayers have asymmetric distribution of lipids
i. The outer layer has more bulky lipids like gangliosides and
sphingomyelins
Glycolipids and glycoproteins also face outside for cell
recognition
ii. The inner layer has more compact lipids
Because it bends more in a spherical cell membrane
iii. The loss of asymmetry will have consequences
The flipping of PS from the inside to outside is
observed in apoptosis
c. The lipids move about either by diffusion or catalysed movement by
enzymes
i. They diffuse laterally rapidly, but transversely very slowly
ii. Flippase uses ATP to move lipids from the outer layer to the
inner layer
iii. Floppase uses ATP to move lipids from the inner layer to
outer layer
iv. Scramblase uses Ca2+ ions to randomly flip lipids transversely
d. The lipids either behave like a gel or liquid crystal depending on
composition and temperature
i. When it is gel-like it is thicker with a smaller surface area, and
it less fluid
ii. When it is a liquid crystal, it is thinner with a larger surface
area and is more fluid
iii. Proportions of unsaturated fatty acids and cholesterol will
affect fluidity
More unsaturated fatty acids cause disorder that
increases fluidity
More cholesterol increase order and rigidity by
stabilizing the straight chain arrangement of saturated
fatty acids
9. The lipid bilayer follows a fluid mosaic model with integral and peripheral
proteins and other components

a. The evidence of fluidity comes from diffusion of differently labelled

fused cell membranes, and recovery of photobleached region of
labelled cell membrane
b. While the lipids bilayer forms a boundary between the cell and the
environment, the other components perform other functions
i. Controlled metabolite transport
ii. Signal reception and transmission
iii. Enzymatic reactions
iv. Contact with other cells
v. As anchor for cytoskeleton
c. Integral proteins span the entire membrane through hydrophobic
segments
i. Hydropathy index measures the hydrophobicity of a region of
the protein through the amino acid residues
ii. It is used to find transmembrane domains as they have more
hydrophobic amino acid residues
Integral proteins can have either a single pass
transmembrane region, or multi-pass transmembrane
region
The multi-pass can be due to alpha-helices
entering and leaving the cell membrane
repeatedly
Transmembrane domains are usually alpha helices or
beta sheets
d. Peripheral proteins are non-covalently associated with polar groups
of lipids and integral proteins
i. They can be associated directly or indirectly
They associate directly if they have a region that forms
ionic and hydrogen bonds, or have a hydrophobic loops
that enters the cell membrane
They associate indirectly through association with
integral proteins
e. Some membrane proteins can be covalently-linked to lipids to
anchor them to the membrane, forming lipoprotein
i. They can be amide linked or thioester linked
10.As the lipid bilayer forms an partially permeable boundary, membrane
transport can either be unmediated or mediated
a. Unmediated transport is by passive diffusion of small, uncharged
molecules down a concentration gradient without carriers or
proteins
i. The rate is proportional to the differences in concentration
b. Mediated transport can be facilitated diffusion or active transport by
membrane protein transporters
i. Transporters can be uniport, symport or antiport
Uniport transporters only allow one molecule to move
in one direction
Symport transporters allow two molecules to move in
the same direction
Antiport transporters allow two molecules to move in
opposite directions
ii. Facilitated diffusion uses transporters to mediate passive
diffusion down a concentration gradient

This increases the rate of diffusion

The transporter has a passive channel or can undergo
conformational change
No ATP hydrolysis despite conformational
change
Binding of target molecules triggers the
conformational change
It gets released through diffusion at the
less concentrated side
The transporters can become saturated limiting the
rate of diffusion
The rate will still be greater than that of
unmediated transport
The transporters can be highly selective and gated
Allows a specific molecule to move in only on
direction
Selectivity can be due to charges attracting a
specific target molecules, and narrow diameter
to exclude larger molecules
Gates can respond to pressure, ligands, signals
and voltage
iii. Primary active transport moves molecules against a
concentration gradient with ATP hydrolysis
ATP is used to phosphorylate the transporter that
causes a conformational change
The added phosphate is then hydrolysed to restore the
original conformation
iv. Secondary active transport uses existing ion gradient to drive
the unfavourable transport of the target molecule
ATP is used to maintain the ion gradient instead of
transporting the target molecule
The target molecules moves when the ion
moves, either through a symport or antiport
The Na+/glucose symport allows glucose to be
transported against its concentration gradient through
the Na+ gradient that is maintain by Na+/K+ ATP pump
Carbohydrates
1. Carbohydrates are the most abundant biological molecule containing 3
carbons or more
a. There is one carbonyl group (ketone or aldehyde) and the each
other carbon contains a hydroxyl group
b. General formula is (CH2O)n, where n is greater than or equal to 3
c. They perform several functions
i. As an energy source
ii. As structural materials
iii. For signal recognition
2. Monosaccharaides are classified depending on their carbonyl group,
whether it is an aldose or ketose, and the number of carbons
a. They exist as stereoisomers and bend polarized light

i. Due to the non-carbonyl or terminal carbons being chiral

centers
ii. The isomer is drawn using Fischer projection
The C=O bond is drawn facing the right
The stereoisomer form is determined by the highest
numbered chiral carbon
The carbon furthest from the carbonyl group
that is not terminal (since terminal has two
hydrogens)
It is D(+) if the hydroxyl group is on the right,
the same side as the carbonyl group
It is L(-) if the hydroxyl group is on the left, the
opposite side of the carbonyl group
iii. The number of stereoisomers of aldoses are determined by
2n-2, where n is the number of carbons
Since the carbonyl carbon and terminal carbon are not
chiral centres
iv. The number of stereoisomers of ketoses are determined by
2n-3, where n is the number of carbons
Since there are two terminal carbons that are not chiral
centres
b. Monosaccharides usually exist in cyclic form, since the carbonyl
group can react with the hydroxyl group to form a hemiacetal or
hemiketal
i. Majority of monosaccharides exist in cyclic form
Either in boat or chair conformation
Chair conformation is the one taught in CM1401
and is more stable than boat
Only aldohexoses can have the bulky terminal
carbon in the equatorial position
ii. The carbon originally with the carbonyl group becomes the
anomeric carbon as the new hydroxyl group can project
above (beta) or below (alpha) the ring
Formed in equal proportions
For aldoses it is carbon 1, for ketoses it is carbon 2
Cyclic ketoses have a terminal carbon bonded to the
anomeric carbon rather than a hydrogen
iii. The carbonyl group will attack the second last carbon instead
of the terminal carbon because it is more stable to do so
Monosaccharides usually form 5-sided (furan) or 6sided rings (pyran)
Aldopentose will form furanose
Aldohexose will form pyranose
c. Monosaccharides have several derivatives
i. It can be oxidised to form sugar acid
ii. It can be reduced to form sugar alcohol
iii. It can undergo esterification to form sugar ester
iv. One hydroxyl group can be removed to form deoxy-sugar
v. It can undergo amination to form amino sugar
3. Disaccharides are form when the anomeric carbon in a cyclic
monosaccharide forms a glycosidic bond with another monosaccharide

4.

5.

6.

7.

8.

a. An alpha glycosidic bond causes the other monosaccharide to have

the hydroxyl group on its anomeric carbon to be on the same side
as the attacking monosaccharide
b. A beta glycosidic bond causes the other monosaccharide to be
flipped such that the hydroxyl group on its anomeric carbon is on
the opposite side as the attacking monosaccharide
c. Alpha or beta glycosidic bond can only be formed when attacking
any carbon other than the terminal one, since it is achiral
i. Alpha or beta-1,4-glycosidic bond but only alpha-1,6glycosidic bond for glucose
Polysaccharides are formed from the linkage of multiple monosaccharides
and their derivatives
a. Branching can be present through glycosidic bonds forming on the
terminal carbon
b. The polysaccharide can also be linked to other compounds to form
glycoproteins and glycolipids
Starch and glycogen are formed from glucose polymerising into linear
amylose and branched amylopectin
a. Amylose is formed from only glucose alpha 1,4 linkages while
amylopectin also contain glucose alpha 1,6 linkages
b. Starch branches about one every 12-30 residues, while glycogen
branches once every 8-12 residues
c. The linear amylose can form helical structures, like alpha helix in
proteins, due to the bond angle in alpha glycosidic bonds
i. Iodine can be inserted into the amylose helix causing starch
to be stained
d. They function as storage compounds as the alpha-glycosidic bonds
can be hydrolysed at the reducing end to release glucose units
Cellulose is formed from glucose polymerising into sheets through beta1,4 glycosidic bonds
a. These bonds are straight thus allowing the formation of extended
linear chains
i. Interchain hydrogen bonds allows the formation of sheets
ii. Intersheet hydrogen bond gives cellulose structural strength
iii. Intrachain hydrogen bonds can also form
Polysaccharides can be linked to peptides, forming peptidoglycans, in
bacterial cell walls, leading to gram positive or gram negative bacteria
a. If the peptidoglycan are exposed, the bacteria is gram positive.
b. Else if the peptidoglycan is sandwiched between two lipid bilayers,
the bacteria is gram negative
c. The crosslinkage between peptidoglycans, either directly or
indirectly, confers structural rigidity
Glycoproteins are proteins that are covalently linked to oligosaccharides or
polysaccharides groups
a. Linked by O- or N-linkages
i. O-linked glycoproteins are found in mucin and cell surface
glycoproteins
The polysaccharides help to keep the protein
extended, or keep a globular head extended
ii. N-linked glycoproteins are used for sorting signals, for protein
folding and stabilization or cell surface recognition

b. Glycosylation of proteins occur in the endoplasmic reticulum and

golgi network
i. O-glycosylation occurs only in the Golgi apparatus
ii. N-glycosylation occurs in the ER and Golgi
c. Proteoglycans are a class of glycoproteins that consists primarily of
glycosaminoglycans
i. Glycosaminoglycans are polymerised amino sugars with
carboxyl or sulphate groups replacing the hydroxyl groups
ii. They are attached hyaluronic acid in cartilage, and interact
with water to provide flexibility and shock resistance
iii. Proteoglycans can also bind to growth factors to increase
local concentration
iv. They can also bind to the extracellular matrix for cell
adhesion
Respiration
1. Glucose is an important sugar molecule as it is used for respiration
a. The catabolism of glucose produces intermediates for synthesis of
substrates for energy production
2. Glycolysis is the first part of cellular respiration
a. Glycolysis modifies the glucose for several uses
i. It can produce pyruvate for anaerobic respiration to produce
ATP without oxygen
ii. It can produce acetyl-CoA for use in the citric acid cycle for
aerobic respiration to generate ATP
iii. It can also provide intermediates for other biosynthesis and
regulation processes
b. Glycolysis occurs in all cells, in their cytoplasm
i. Some cell have no mitochondria and solely rely on glycolysis
for ATP production
c. Glycolysis occurs in two main steps
i. Glucose is first trapped in the cell, and then cleaved into two
three carbon units
Glucose is phosphorylated using ATP to form glucose-6phosphate that cannot freely leave the cell
Hexokinase catalyses the irreversible reaction
Hexokinase is product inhibited
A specialized form, glucokinase in liver
allows high activity without product
inhibition
Glucose-6-phosphate is then converted to its isomer,
fructose-6-phospahte
By phosphor-glucose isomerase
Fructose-6-phosphate is then further phosphorylated to
form fructose-1,6-diphosphate
By phosphor-fructokinase I
This is an irreversible step and a major point of
regulation
Fructose-1,6-diphosphate is then cleaved to form
glyceraldehyde 3-phosphate (G3P) and
dihydroxyacetone phosphate (DHAP)

 By aldolase
DHAP can be converted to G3P by triose phosphate
isomerase
G3P is used in the next part of glycolysis
ii. ATP is then generated through substrate level
phosphorylation
G3P is oxidised by NAD+ and Pi to give 1,3bisphosphoglycerate
By glyceraldehyde 3-phosphate dehydrogenase
Also produces 1 unit of NADH for every unit of
G3P
1,3-BPG then undergoes substrate level
phosphorylation to produce 3-phosphoglycerate
By phosphoglycerate kinase
Also converts 1 unit of ADP to ATP for every unit
of G3P
3-phosphoglycerate is then converted to a higher
energy intermediate, phosphoenol-pyruvate
Isomerism by phosphoglyceromutase
Dehydration by enolase
Phosphoenol-pyruvate then undergoes another
substrate level phosphorylation to produce pyruvate
By pyruvate kinase
Also converts 1 unit of ADP to ATP for every unit
of G3P
This is another major point of regulation
d. Overall,

++ 2 ATP+2 H 2 O
++2 Pi+ 2 ADP 2 pyruvate+2 NADH + 2 H
glucose+2 NA D

i. Glycolysis consumes 2 ATP but generates 4 ATP for a net gain

of 2 ATP.
ii. 2 units of NADH is also generated per unit of glucose that will
be used to regenerate NAD+ in either anaerobic or aerobic
respiration
3. Under anaerobic conditions, pyruvate is reacted to form different products
to regenerate NAD+ for glycolysis to continue
a. In animals, lactate is produced from pyruvate with the use of NADH
i. The reaction is catalysed by lactate dehydrogenase
b. In yeast, ethanol is produced from pyruvate with the use of NADH
i. The reaction is catalysed by alcohol dehydrogenase
4. The tricarboxylic acid (TCA) cycle, aka citric acid cycle, generates NADH
and FADH2 for oxidative phosphorylation (which uses oxygen and
regenerates NAD+) in the mitochondria
a. The TCA cycle performs several functions
i. It generates energy directly with GTP, and indirectly with
NADH and FADH2
ii. It provides intermediates for biosynthesis
iii. It provides feedback regulation to other pathways through
regulating citrate levels
b. The enzymes for the TCA cycle are located in the mitochondria

i. Succinic dehydrogenase (SDH) is found as part of a complex

in the mitochondrial inner membrane, but does not span the
membrane
ii. All other enzymes are found in the matrix
c. The TCA cycle links with glycolysis through the dehydration of
pyruvate to acetyl-CoA
i. The pyruvate dehydrogenase (PDH) complex consists of three
enzymes
E1 requires thiamine pyrophosphate as coenzyme
E2 requires lipoate and coenzyme-A as coenzymes
E2 requires FAD and NAD+ as coenzymes
ii. This is an irreversible reaction that is a major point of
regulation
iii. This reaction produces 1 unit of NADH with every unit of
pyruvate
iv. Overall:

+
++Coenzyme A Acetyl CoA +C O2 + NADH + H
pyruvate+ NA D

d. Acetyl-CoA will then enter the TCA cycle

i. It first undergoes an irreversible condensation reaction with
oxaloacetate to form citrate
With citrate synthase and coenzyme A as by-product
There is product inhibition by citrate
ii. Citrate is then rearranged into its isomer, isocitrate
By aconitase
Isocitrate has two out of three carboxyl groups
available for decarboxylation
iii. Isocitrate undergoes oxidative decarboxylation to form alphaketoglutarate
By isocitrate dehydrogenase
Uses NAD+ and produces NADH, H+ and CO2
Is rate limiting and a major point of regulation
iv. Alpha-ketoglutarate undergoes further oxidative
decarboxylation to form succinyl-CoA
By alpha-ketoglutarate dehydrogenase
A complex of three enzymes that require the
same prosthetic groups as PDH
Uses coenzyme-A and NAD+, and produces NADH, H+
and CO2
v. As succinyl-CoA has a high energy thioester bond, substrate
level phosphorylation occurs to generate GTP and succinate
By succinate thiokinase
Uses GDP and Pi, and produces GTP and coenzyme A
vi. Succinate gets oxidized to fumarate
By succinate dehydrogenase, found in the inner
mitochondrial membrane
Uses FAD and produces FADH2
vii. Fumarate gets isomerised to malate
By fumarase

viii. Malate gets oxidised to oxaloacetate, regenerating it as a

catalyst
By malate dehydrogenase
Uses NAD+ and produces NADH, H+
ix. Overall:

++ FAD H 2 +GTP
++ FAD+GDP 2C O 2+Coenzyme A+3 NADH +3 H
AcetylCoA +3 NA D

5. Oxidative phosphorylation generates ATP from NADH and FADH 2 from

glycolysis and the TCA cycle
a. The necessary protein complexes are found in the inner membrane
of the mitochondria
i. The lipid bilayer is impermeable to protons, NADH and FADH 2
ii. NADH produced outside of the mitochondria during glycolysis
enters through 2 shuttles
Glycerol-3-phosphate converts NADH + H+ from the
cytoplasm into FADH2 in the mitochondria
Maltate-asparate transports NADH + H+ from the
cytoplasm into the mitochondria matrix as it is
b. Oxidative phosphorylation works by generating a proton motive
force through the pumping out of protons from the mitochondria
i. The electron transport chain uses two carriers, Coenzyme Q
and cytochrome C
ii. NADH + H+ reacts with complex I, NADH-Q oxidoreductase,
and CoQ to produce NAD+ and CoQH2
In the process, 4 protons are pumped out by the
complex
iii. FADH2 reacts with complex II, succinate-Q reductase, and CoQ
to produce FAD and CoQH2
In the process, no protons are pumped out by the
complex
iv. CoQH2 from both processes then react with complex III, Qcytochrome c oxidoreductase, and cytochrome c, to produce
CoQ and reduced cytochrome c
In the process, 4 protons are pumped out by the
complex
v. 2 units of reduced cytochrome c then reacts with complex IV,
cytochrome c oxidase, and 1 atom of oxygen to produce
oxidised cytochrome c and water
In the process, 2 protons are pumped out
vi. The proton gradient across the inner mitochondrial
membrane causes protons to flow through ATP synthase that
catalyses the formation of ATP from ADP and Pi
ATP synthase has two major areas
The F0 pore forms a channel for the movement
of protons cross the inner membrane
The stalk in the F1 headpiece then uses the
energy from the movement of protons to rotate
This induces conformational changes in
the subunits in the F1 headpiece, driving
the release of ATP

Each rotation of the stalk requires 10 to

14 protons, and produces 3 ATP molecules
vii. Each molecule of NADH results in 2.5 molecules of ATP
produced
viii. Each molecule of FADH2 results in 1.5 molecules of ATP
produced
6. Overall, one molecule of glucose produces 2 ATP, 2 GTP, 10 units of NADH
+ H+, 2 units of FADH2
a. Using the glycerol-3-phosphate shuttle, the 2 units of NADH outside
the mitochondria is converted to FADH2
b. Overall, 28 units of ATP and 2 units of GTP is produced
i. 30 units of ATP if the outside NADH is brought in by the
maltate-asparate shuttle instead
7. There are several major points of regulation for respiration
a. Phosphorylation of fructose-6-phosphate to fructose-1,6diphosphate
b. Substrate level phosphorylation of phosphoenol-pyruvate to
pyruvate
c. Dehydration of pyruvate to acetyl-CoA in the matrix for the TCA
cycle
d. Oxidative decarboxylation of isocitrate to form alpha-ketoglutarate
Questions
1. Difference between beta hairpin and beta turn?
2. Are domains considered to be a type of super-secondary structure, or a
tertiary structure? Can proteins have more than one tertiary structure?
3. Why does gene duplication in paralog eventually gives rise to different
functions?
4. Why does negative effector binding to an allosteric protein increase Vmax?

Miscellaneous
1. Concentration of water is 55 M, since there are 55 moles of water in 1 litre
of water
a. 1000g/18 = 55.55556