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Biochemistry lecture notes
Lecture 1:
• Central dogma: cell information flows from DNAà RNAà Protein
• DNA replicates, then gets transcribed into RNA, and then translated into proteins (chain of
amino acids)
• 20 major amino acids
o only L forms are found in our cells, D-forms are found in bacterial cell walls
o 4 classes of amino acids:
§ Polar: negative charge/ acidic
§ Polar: positive charge/ basic
§ Polar: uncharged
§ Non-polar
o The properties of the side chain that determine the protein’s character include:
1
...
Physical size
3
...
e
...
6 residues per turn
o 0
...
e
...
e
...
Heating
• Protein families:
o During evolution, new proteins come from old ones
o Protein family is related by evolution, they have similar primary sequence, structures,
functions and domains

•

•

o Amino acid residues that are necessary for function are found in all organismsà thus, a
common protein sequence in a all organisms means that it’s a protein from evolution that
has been conserved because it is necessary for organism’s function
§ Called “conserved residues”
§ Example: steroid hormone receptor
Ligand binding proteins:
o Many proteins contain sites to which ligands specifically bind and form a complex with
the protein
o Ligand: molecule that can form this complex
o Binding occurs by multiple weak or a few strong forces
o Ligand binding is extremely specific to the protein’s binding site
o Example: hemoglobin is an iron-containing oxygen transport metalloprotein in the red
blood cells of all vertebrates—it binds specifically to iron in order to carry its function of
transporting oxygen
Ligand binding-dissociation constant
o Dissociation constant (Kd): a measure of the affinity of an interaction between a ligand
and a protein
o An equilibrium constant
o For a protein (P) binding ligand (L)

o High affinity=tight binding= small Kd value
o Units are M (concentration)
**Remember the smaller the Kd value, the higher the affinity!!
• The ribosomal complex is made up of RNA, protein, and tRNAs
Lecture 5: Collagen and Antibodies
Collagen: 300nm long & 1
...
), collagen drinks, acne treatments
• Collagen helical folding:
o Presence of so much proline prevents alpha helix
o Instead, forms a poly-proline type 2” helix
§ More extended than alpha helix
§ No intra-chain H bonds

•

•

•

•
•

§ Stabilized by steric repulsion of proline side chains
§ 3 residues per turn
o Must be first synthesized as a precursor which is soluble called “pro-collagen”
§ Consists of 3 polyproline type 2 helices
Pro-collagen triple helix:
o No internal hydrogen bonding
o Amide N and O atoms are too far apart
o Steric repulsion between prolines
Poly-proline type 2 helix:
o Mainly proline, hydroxyl-proline, and glycine
o Collagen has characteristic sequence
o Every third residue is G
o Lots of prline and hydroxyl-proline
§ Modified amino acid with hydroxyl group
§ The hydroxylation of proline residues plays a role in triple helix stabilization of
collagen molecules
§ Hydroxyl-proline: OH groups can form H bonds to help keep triple helix
together
§ Hydroxy-Lysine: OH groups serve as sites of sugar addition
§ Lysines: involved in a cross-linking reaction that creates covalent bonds between
collagen fibrils
o Example: in type 1 human, sequence is TGSPGSPGPDGKTGPPGPAGQDGRPGPPGP
** The three chains are hydrogen bonded to each other, the hydrogen bond donors are the
peptide NH groups of glycine residues—The OH groups on hydroxyproline can also
form hydrogen bonds
Properties:
o Glycine in every third position is ESSENTIAL
§ Any other amino acid pushes chains apart
o Gives a thin (1
...
e
...
100 residues
B sheets
Disulfide links two sheets
Hydrophobic center
IgG functional segments can be separated by proteolysis yielding 3 fragmentsà 2 fab (fragment
antigen bonding) & 1 Fc (fragment crystallized—an effector site that mediates function)
Ø The Fab-antigen complex consists of the antigen, and the heavy and light chain
components of the Fab—antigen binds to both the heavy and light chains
Activate the complement pathway
Production and use of antibodies:
o Created by injecting an antigen in an animal and then harvesting the antibodies in the
blood (created by the animal’s immune response)
o Extreme specificity makes IgG a valuable tool
§ Laboratory experiments: identification of molecules in mixtures

§
§

Clinical diagnosis of disease (i
...
HIV)
Clinical therapy (i
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antibodies against venoms)

Lecture 6: Enzyme catalysis
• Enzymes: biological catalysts
• Perform nearly all chemical transformations in cells
• Accelerate, but are unchanged by a reaction
• DO NOT get used up in a reaction
• Most enzymes are proteins
• Name often ends in “ase”
• Often extremely specific—the have targeted or restricted ligands (substrates)
Types of chemical reactions carried out:
o Hydrolytic: cleavage using water
§ Nucleases, proteases, phosphatases
o Condensation: connect molecules together
§ Polymerases, synthases
o Isomerization: re-arrange bonds
§ Isomerases
o Oxidation: gain or loss of electrons
§ Oxidases, reductases, de-hydrogenases
o Group transfer: transfer chemical groups
§ Phosphorylation, sumolvation, acetylation, glycosylation (N/O linked)
• Active site of enzymes are the part of the enzyme where the reaction with its substrate takes
place
o Active site is a small part of the enzyme’s surface (5% or less)
o Substrate binds in active site
§ Multiple weak bonds
§ Dissociates from enzyme
• Enzymes catalyze reactions by lowering the activation energy of the reaction
o Transition state: the intermediate form of the reactant before it turns into product
§ Highest energy state along the reaction coordinate
§ Different from both reactants and products
§ At this point, molecules will always go on to form products
o The speed of a reaction is determined by how difficult is it to get to the transition state—
enzymes make it easier to get to the transition state, thus, speed up reactions
• Enzyme catalytic mechanisms:
o Highest affinity of enzyme is for the transition state, and not the substrate or product
o Binding of the substrate pushes the enzyme towards the transition state, resulting in a
strain on the substrate
o Enzymes work best at specific temperatures and pH
• Induced fit hypothesis
o The initial interaction between the enzyme and substrate is relatively weak
o These interactions induce conformational changes in the enzyme that strengthen binding
o The enzyme changes conformation and increases the affinity to reach the transition state,
stabilizing it and thereby reducing the activation energy required

Kinetics vs
...
Enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to
occur between them
2
...
Enzyme strains the bound substrate molecule, forcing it toward a transition state to favour a
reaction
•

Transition state analogues:
o Compounds that resemble the transition state, but do not undergo a chemical reaction
§ Similar geometry, charge distribution etc
...

§ Can help discover how an enzyme works
o Rate of reaction will depend on various factors such as the affinity of enzyme for
substrate and substrate concentration
o Plotted on a velocity vs substrate concentration plot

o Michaelis Menten equation:
§ Described the kinetics of the E-S complex, ie
...
1/[S], gives a double-reciprocal/
Lineweaver-Burk plot (straight line)

•

Enzyme Inhibition:
o Therapeutic drugs, natural inhibitors of metabolism, herbicides and pesticides
o Two general types:
§ Reversible: binding of inhibitor to enzyme non-covalently, inhibitor can be
removed (i
...
competitive inhibitor)

§ Irreversible: covalent bond formed with enzyme, permanently blocks activity
o Competitive inhibition:
§ A type of reversible inhibitor
§ Binds to active site and has a similar structure to substrate or product
§ Blocks access to substrate
§ Increases KM but does not change Vmax
§ Large excess of substrate overcomes inhibition
§ Reduces the concentration of free enzymes available for substrate binding**

Summary:
• Enzyme reaction rates vary with substrate concentration
• Can be described with both KM and Vmax
• Kinetic analysis can give insight into enzyme mechanisms
• Development of enzyme inhibitors have various uses
Lecture 8: Protein purification
Uses:
1
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e
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To study the structure and function: difficult to understand activity in mixtures, must be pure
to determine structure
3
...
;
thus, need to remove these unwanted materials (“contaminants”)
o Proteins may differ in many properties: size and shape, charge, location, surface
hydrophobicity
o When purifying, need to first choose an assay method (depends on protein of interest
and mixture—must be able to detect the protein in the mixture and measure the property
of interest) & starting material (i
...
human tissues, plants, bacteria etc
...
analytical methods:
o Both are used to purify proteins, start with preparative method, follow with analytical
o Preparative methods: used to homogenize (bust up) materialà large scale (mg to kg)
and divide mixture into fractions
1
...
Centrifugation: spinning the homogenate to separate by size/densityà
differential centrifugation
Ø Low speed: 100 to 1000 x g (force of gravity)à used for whole
cells and nuclei, large debris are pelleted
Ø Medium: 2000 to 50000 x g à used for mitochondria and
lysosomes
Ø High: 60000 + x g à used for ribosomes, viruses, large
macromolecules
3
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e
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Column Chromatography Types
• Ion exchange
• Gel-filtration
• Affinity chromatography
** Need to know their mechanisms
SDS-PAGE (SDS Polyacrylamide Gel Electophoresis)
• Most common analytical method
• SDS= sodium dodecyl sulfate—an ionic detergentà a long hydrocarbon chain attached to a
sulfur through an ether bond, where sulfur is attached to 3 other oxygen and a sodium is present
beside the one negatively charged oxygen
• Separates on basis of polypeptide chain size
• Charges molecules migrate in an electric field
• A gel acts as a molecular sieve, smaller molecules go faster
• Gel is made of polyacrylamide (6%-15%)—a hydrophilic polymer in long chains
• SDS used to denature proteins and give a negative charge
• Gels can be single concentrations (i
...
6% or 12%) or a gradient (6%-15%)
• Low % gels used for high MW proteins
• Higher % gels used for low MW proteins
• Gradients used when want to examine a range of different sized proteins
• Process:
a
...
Makes proteins unfold into a linear shape and gives a negative charge
b
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Proteins are then placed for electrophoresis on gel
i
...

o Finally, after the protein molecules have been separated, bands representing molecules of
different sizes can be visualized

TOPIC 9: Lipids and biological membranes
• Lipid: a biological that is insoluble in water
• Fatty acids: used for energy and structure
o A long hydrocarbon chain with a carboxylic acid at the end
o Saturated: no double bonds, all carbons are single bonded to H and other C
o Unsaturated: 1 or more double or triple bonds

•
•
•

In living organisms, cis fatty acids are most dominant
The first double bond normally goes between the 9th and 10th carbon (not random usually)
Cis forces the chain to have a bend in it—real representation:

•

•
•
•

Short forms to refer to fatty acids:
o 16:0 is a linear saturated 16 carbon chain
o For unsaturated (all these options can name the same thing):
§ 16: 1c Δ9 (1 cis bond at the 9th C)
§ 16:1 (n-7)
§ 16:1 (w-7)
§ 16:1
fatty acid saturation and blood cholesterol
LDL= low density, lipoprotein, carries cholesterol to tissues
HDL= high density lipoprotein, scavenges cholesterol from tissues

Dietary Fat
saturated
Cis-unsaturated
Transunsaturated

Effect on LDL
increase
decrease
increase

Effect on HDL
increase
increase
decrease

Overall effect
even
good
bad

Types of Lipids:
1
...
Glycerophospholipids: used in membranes
• Glycerol+fatty acid+ phosphate group
3
...
Includse ceremids, sphingomyelin
b
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e
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e
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passive transport:
o Passive: molecules moves down electrochemical gradient (going from high
concentration to low concentration or positive and negative gradients/ voltage gradients)
§ Can be facilitated or not
o Active: molecule move against electrochemical gradient with the use of ATP
§ Can be primary (directly uses ATP) or secondary (indirectly uses ATP)
**Application: toxins target ion channelsà the venoms of poisonous animals contain small peptides
which can bind to ion channels in order to disrupt their function, this causes the prey to be paralyzed
(ex
...
e
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Multi-drug resistance proteins)
à proteins can also span membranes as beta-sheets, hydrophic exterior
and hydrophic interior
§ Monolayer- associated alpha helix: proteins in the membrane but don’t actually
poke all the way through, only visible on one side of the membrane
§ Lipid linked: the protein does not actually go into the membrane, however, they
are modified with a lipid part that sticks into the membraneà this causes the
protein to stick in place and stay connected to the membrane (consider the protein
to be in the membrane because of the lipid part that is now part of the protein and
present in the membrane)
o Peripheral proteins: on the outside of the membrane, associated with a molecule that is
in the membraneà associated with the membrane but NOT actually touching the
hydrophobic part of the membrane
§ Protein attached
** It is very hard to isolate integral membranes because they are amphipathic, thus, need to always
disrupt the membrane in order to isolate ità need to add detergent in order to isolate them because they
will protect the hydrophobic part of the protein so they can be in the hydrophilic area without denaturing
or clumping together
•

**However, peripheral membrane proteins are easier to isolate because need to find a condition to
detach the protein from the molecule imbedded in the layer that it is stuck too (disrupt their bonding)à
never actually need to disrupt the bilayer itself though
Summary:
• Membrane proteins comprise 50% of biological membranes by mass
• Classes of membrane proteins include transporters, receptors and enzymes
• Facilitated transport by transporters or channels can be active or passive
• Proteins may be membrane-integral or membrane-peripheral; most Transmembrane proteins
cross the membrane as alpha helices
• Membrane proteins can diffuse in the bilayer unless restricted:

TOPIC 9: Carbohydrates
• Four main classes of biomolecules:
1
...
Fatty acidsà fats and membrane lipids
3
...
Nucleotidesà nucleic acids
• Sugars are monosaccharaides of carbohydrates
• Polysaccharides are many sugars together that make up carbohydrates
Monosaccharaides:
• Monosaccharaides: smallest unit of carbohydrates
o General formula: (CH2O)n
o Represented by Fischer projections: L and D
o Most have a D configuration at the highest numbered chiral carbon

o Some hexoses:
§ Aldoses: glucose, galactose, mannose, fructose
§ Ketoses: fructose
o Most monosaccharaides form ring structures (cyclization)

**C1 looses double bond to O and makes a new bond with the O attached to C5—C1’s O takes the H
from C5’ O in order to have a neutral charge
o Cyclized mono
...
beta linkages:
o Number the carbons starting closest the anomeric carbon, know if something is alpha or
beta by comparing the O in linkage to the highest number carbon
§ Beta: if both O and highest number carbon are down/up
§ Alpha: if O and highest carbon are on OPPOSITE sides (one is down and the
other is up)
Polysaccharides:
• Many monosaccharides joined together
• Used as energy storage in the form of glycogen and starch
• Glycogen: chains of 12-14 glucose monomers joined in alpha 1,4 linkage
o Interior chains have 2 branch pointed with alpha 1,6 linkages
o First chain is covalently attached to the protein glycogenin
o When you run low on glucose, you break down this molecule in order to release glucose
molecules in the body
o Structure:
§ Glycogen molecule is a bunch of glucoses joined by a 1,4 glycosiding linkage and
these glucoses are also joined up through 1,6 alpha linkages
•

à Bottom linkages are alpha 1,4
Starch: composed of amylose (20-30%) and amylopectin (70-80%)
o Example: potato, high in energy
o Amylose units are connected in alpha 1,4 polyglucose linkages, very few branch points
o Amylopectin units are connected in alpha 1,4 polyglucose linkages, approximately 5% of
monomers are involved in alpha 1,6 linkages
o Humans easily digest glycogen and starch
o Same essential type of linkage as glycogen, used in plants as energy storage source
• Polysaccharides are used as structural molecules in the form of cellulose, chitin, and pectin
o Cellulose: unbranched beta 1,4 polyglucose
o Chitin: unbranched beta 1,4 polymer of N-acetyl-B-glucosamine
o Pectin: unranched alpha 1,4 polymer, mainly of D-galacturonic acid, partially
methylated
§ Poorly digested by humans—dietary fiber (found in vegetables)à we don’t have
the enzymes to digest B linkages, so we cannot get any energy from the
polysaccharide and properly digest it—good for you because you have some
roughage going through your system, cleaning it out
§ We are also unable to digest molecules that are methylated
§ What is the difference between fibre and other carbohydrates? Fibre are a type of
carbohydrates that you cannot digest, the other carbohydrates are mostly made up
of starch and get stored as glycogen—these can provide us with energy
Oligosaccharides:
• Molecule is made up of a very small number of monosaccharides
• Used for cell coating—protect the cell and cushions the brain from damage
• Sugars are covalently attached to lipids and membrane proteins
• Protect cells and make them slipperyà makes it easier to go through capillaries in the body
• Can be used for cell to cell recognition
o Different cells can have different sugars attached to them
o Sometimes we have an infection and we can deal with it by bringing in a neutrophil that
has oligosaccharides attached to it—proteins recognize these oligosaccharides and know
that there is a neutrophil present
o Also used in embryonic development
•

Cell coating:

Cell-cell recognition:

Summary:
•
•
•

Monosaccharides have the general formula
and can exist in non-cyclic or cyclic
forms
Monosaccharides can be coupled through O-glycosidic bonds to form polysaccharides
Polysaccharides have several biological functions, including energy storage, formation of
structures and cell-cell recognition

TOPIC 10: Biological Forms of energy and reducing power
• Gibbs free energy: indicates the amount of work available in the system, the reactants have a
certain amount and the products have a certain amount, thus, delta G is the difference between
their values and determines whether a reaction is energetically favourable or not
• Whether this is negative or positive can determine whether the reaction will be spontaneous or
not
• Delta G depends on the type of products and reactants (properties of molecules), the reaction
conditions (temperature, pressure, concentrations)
• Energy favourable reaction:
o SPONTANOUS
o Products are favoured, net conversion of reacts to products without the use of energy
o Products have a lower G value than reactants
o Don’t need to do anything in order to make the reaction happen, just happens on its own
o Concentration of products rises whereas the concentration of reactants decreases, thus,
the G value for the products rises and G value for reactants gets slower
o Reaction equilibrium:
§ Eventually, it will reach equilibrium where the reactants and products have the
same G values, thus, the backward and forward reactions are happening at the
same rates—appears as if nothing happening

•

§ At this point G=0
o Le Chatelier’s principle:
§ If an external force acts on the system, reaction shifts to counteract changes in
concentration in order to return back to equilibrium
§ Demonstrates that reaction is reversible-- **Sensitive to changes in
product/reactant concentrations
§ For example, if add more products to the system, the system will shift to favour
the reactant sides—thus making more reactants to level out their concentrations
**Irreversible reactions:
§ Spontaneous, energetically favourable
§ Products are extremely strongly favoured—have an extremely lower G value
(very negative) than reactants
§ The backward reaction is so uncommon that in essence it only goes in one
direction; reactantsà products
§ Insensitive to changes in concentration
§ No matter what you do, it doesn’t matter because the G value of the products
continue to stay very negative
o If a reaction does not proceed to equilibrium, it indicates that it is an irreversible
reaction
Energetically unfavourable reaction:
o Reactants are favoured, they have a lower G value than the products
o Non-spontanous, need energy input in order to make it happen
o Changing concentrations enough to favour products may not be possible
o Enzymes change the kinematics of a reaction, however do not change the
thermodynamics of the reaction—thus, the enzyme does not make a reaction
spontaneous, it just helps it proceed!!
§ Enzymes help reactions faster but do not change the direction of reaction
§ They lower the activation energy but do not actually change the relative G
§ If a reaction is favourable in backwards reaction, it will simply go faster in the
backward direction
§ Thus, enzymes can ONLY be used with a energetically favourable forward
reaction if you desire the the forward reaction to happen
o This is where reaction coupling solves the problem of making unfavourable reactions
become favourable
o An energetically favourable reaction can be used to make unfavourable reaction
proceed
o The reactions must be chemically coupled together
o Favourable reaction is one with a negative G value, thus coupling a very negative
reaction and a smaller positive reaction will result in a negative G value
o However, you do not want to use way too much energy because most of the energy
would be wasted as heat
o Thus want to find a reaction that has a negative value close to the positive value of
the reaction of interest
o Cells store energy from food in carrier molecules, to be spent a little energy at a
time—conserving their energy

**Analogy: if you’re not going to be given change, and have $100 and only need to buy something
worth $18, go to bank and break it up into $20 dollar bills, so only waste $2 of your money rather than
$82 dollars
...
3kcal/mol
o In Body, the G for ATP is different because the conditions in the body are different than
the standard conditions—need to know the relative concentrations and temperature of the
body in order to determine à in actual fact, the G in body is less than -7
...
There a lot of negative charges that don’t like to be near each other, thus, by breaking off the
phosphate you allow the negative charges to be more spread out of each other
2
...
Since the more resonance structures you can draw, the more stable the molecule—in the
products you can draw more resonances

3
...
The ratio of ATP is much higher than ADP in the cell, thus, this makes making ADP from ATP
much more favourable
**ATP is said to have “high-energy” phosphoanhydride bonds because of it’s position relative to
o It’s in a position that if you let it go, it will go from high energy to low energy spontaneously
o Bond is situated in the molecule in a way that makes is in a high energy state
à Analogy: a marker itself does not have any more energy than other identical markers of the same
make, colour etc
...
9kcal/mol) however this is minimal compared to the use of other
molecules which is why ATP is often used
What if we need more energy than what ATPà ADP supplies?
• Option 1: Hydrolysis ATP to AMP and 2 Pi
o Gives you a little more than double the energy (-15
...
3kcal/mol, results in creative and inorganic
phosphate
Note of Kinetics vs
...
Glycogen synthesis and breakdown
o Carbohydrate gets stored as glycogen
o Long distance runners “carbo-load” before races in order to have the most amount of
energy available during the run
o Process: G6Pà G1Pà Glycogen (step 1 is reversible whereas step 2 is irreversible)
§ For reversible steps, it’s the same enzyme catalyzing both directions and it simply
goes in the direction that will achieve equilibrium (dependent on concentrations)
§ Irreversible reactions are ones that use an energy source, it makes the reaction
very favorable (low G value) making it irreversible
o Occurs in your muscle cells and liver cells
NOTE:  Glycogen  phosphorylase  and  
glycogen  synthase  undergo  
different  reactions  and  processes—
they  are  not  opposite  processes  or  
mechanisms—they  are  different!  
*Only  thing  they  have  in  common  is  
opposite  products  and  reactants  

In the muscles:
• G6P is a regulatoràallosterically activates glycogen synthase and allosterically inhibits
glycogen phosphorylase
• This is because if have lots of G6P, want to break it down and don’t want to make more
• ATP is a regulatorà High ATP will inhibit glycogen phosphorylase because if have lots of
energy don’t need to deplete our energy stores
• AMP is a regulatorà High AMP indicates low energy levels in body, thus it activates glycogen
phosphorylase in order to break down glycogen into glucose
• Regulated by phosphorylation
In liver:
• Enzymes are regulated with energy levels of the whole body, rather than it’s own energy needs,
no matter what the energy status of the liver is

•
•
•

Only regulated by Glucose (instead of G6P) where high glucose activates glycogen synthase and
inhibits glycogen phosphorylase
Regulated by phosphorylation
Not regulated by AMP or ATP

Control by Phosphorylation:
• Phosphorylation (via kinase enzyme) causes glycogen breakdown
• Dephosphorylation (via phosphatase) leads to glycogen synthesis
• Insulin leads to dephosphorylation in liver and muscle
• Glucagon leads to phosphorylation in liver ONLY (muscle does not respond to
• Epinephrine leads to phosphorylation in liver muscles (flight or fight response)

Muscle stores for own benefit, liver stores for whole body benefit
Both muscle and liver respond to external signals (muscle responds to epinephrine)
Mechanism of Insulin on Glycogen Metabolism:
Insulin= release means high blood glucose
Glucagon= release means low blood glucose

2
...
Gluconeogenesis
• Occurs in the liver
• Reductive process- uses NADH
• Liver tries to supply glucose when low
• Consumes glycogen storage and after tries to make glucose out of other things in the cell
(uses amino acids, pyruvate, citric acid cycle intermediates)
o Converts them into oxaloacetate which is eventually converted into glucose
• If glycolysis is energetically favourable, how is it possible to do the opposite—
making glucose out of pyruvate?
o Concentrations of substances are different under gluconegonesis conditions,
however the difference in concentrations is not enough for overcoming the large –
G—helps but not enough
o What causes this is the use of certain reactions that proceed by completely
different mechanisms in the glycolysis and gluconeogenesis directions
§ Thus the actual pathway is not just the exact opposite of glycolysis
§ Need completely different enzymes that catalyze the backward reactions
in a different way that is more favourable
§ Thus, both glycolysis and gluconeogenesis can be favourable because they
don’t involve t the exact same reactions—they are different reactions

•
•
•

Most regulation occurs at pyruvate carboxylase hereà that’s why pyruvate kinase also regulates
glycolysis (have regulation at the same number steps in the two reactions)
Like glycolysis, gets regulated mostly at the end at the last step
The regulation of the pyruvate carboxylase and pyruvate kinase are opposite of each other—
don’t want them going at the same time, so when one is turned on the other is turned off (we
don’t want to waste energy)

**Fructose-2,6- biphosphate: a compound that increases in concentration when insulin is\ high in the
blood stream; thus, this is insulin’s message
**As AMP rises, it indicates that there is not a lot of energy in the cell; thus, the cell will want to turn
off gluconeoegenesis because it takes in so much ATP to happen
**If high pyruvate concentration, Le Chatelier’s Principle applies so this process will be favoured
Question: if liver is self-less why does it take into considering it’s own energy (AMP) levels to stop
gluconeogenesis
à This is like an emergency case, it doesn’t want to die, so it will make sure it has enough ATP before
trying to supply the body with glucose

-­‐
-­‐

Every time one is turned on, the other is turned off
This is the case every time you have a process like this that is opposite to each other

Summary of Glycogen and glycolysis:

•
•
•
•

Excess glucose is stores as glycogen in a process that is regulated allosterically and by enzyme
phosphorylation in response to hormones
In glycolysis, 1 molecule of glucose is oxidized to pyruvate, forming 2ATP and 2 NADH
Glycolysis is regulated allosterically and by availability of glucose
Fermentation produce ATP in the absence of oxygen, with no net oxidation of carbon

4
...
e
...
Decarboxylation of pyruvate to form acetyl-coenzyme A (acyl-coA)à3 carbon to 2 carbon
molecule releasing carbon dioxide
2
...

Citric Acid Cycle (TCA Cycle, Krebs cycle):
• 2 carbon molecule from acetyl-coA is dropped off in oxaloacetate (4C) making citrate (6C)
• CoA leaves and goes off to do other carrier jobs—never used up in reactions
• Every time a carbon dioxide is released, an NADH is made
• One turn= 3 NADH, 1 FADH2, 1 GTP
• No ATP is made in krebs cycle, however a similar molecules called GTP is made
• 3 irreversible steps: don’t have enzymes that can do the reversible steps, thus, cycle is
unidirectional overall
• In anaerobic conditions the citric acid cycle will stop because you can not regenerate NAD+ and
FAD from NADH and FADH2 because no oxygen to take their electrons
**Know the net reaction and key players
• Irreversible steps are subject to regulation
o For example, if high NADH concentration and it is the product of an irreversible
reactions, NADH would decrease enzyme activity, thus, decreasing the reaction from
happening/ slowing down the pathway (negative feedback inhibition)
o Even if a specific irreversible reaction in citrate cycle doesn’t directly make NADH, it is
still an overall product of the net reaction of the cycle, thus, the enzyme of the
irreversible reaction will still be slowed down
• Reversible steps are not subject to regulation—not committing
o Thus, high NADH levels are unlikely to have any effect on reversible reactions

Regulation of the citric acid cycle:
1
...
Competitive inhibition by products
3
...
e
...
Flavins (least electronegative)

§
§
§
§

Cofactors that are tightly bound to a protein
Thus, considered a prosthetic group
Accepts 2 electrons and 2 protons
Example of Riboflavin: vitamin B2

2
...
Ubiquinone:
§ A lipid that freely diffuses in the membrane
§ The entire molecule is hydrophibic, however, it does have parts that can accept
electron and protons
§ Accepts two electrons, one at a time
§ Not commonly associated with a protein

4
...
Copper centers (most electronegative):
§ Coordinated by histidine side chains usually
§ One copper can accept one electron (Cuà Cu+)
§ Thus, if two coppers in the complex, the complex can accept 2 electrons

Electron Transport protein complexes:
• All exist in the inner mitochondrial membrane
• Made up of many polypeptide chains
• Electron carriers = cofactors
• Electron flow:
o NADHà 1à Qà3à Cytocrome cà 4à O2
o FADH2à 2à Qà3à Cytocrome cà 4à O2
**NADH and FADH2 go through same pathway but have different entry points! Need to know the
order of the pathway

Complex 1: NADH Dehydrogenase:
• NADH binds to the flavin groups and iron-sulfur centers in the complex, the Transmembrane
area of the complex is able to take the energy from the binding and use it to pump the protons
into the mitochondrial matrix
• NADH has to be in the matrix for the binding to occur
• Accepts two electrons from matrix NADH
• NADHà Flavinà (FeS)n à Q
• Pumps 4 protons across membranes (from matrix to intermembrane space) per electron pair
Complex 3: Cytochrome b-c1 complex:
• Has many subunits of heme, FeS, cytochrome b (in the Transmembrane region)
• Spans the membrane
• Accepts 2 electrons from QH2:

•
•

This process is repeated with a second QH2
Uses the Q cycle to pump protons:
o Steps:
LISTEN TO LECTURE RECORDINGS (approx
...
So 1 matrix NADH allows synthesis of 2
...
5 ATP

Summary – Topic 15
•Electrical potential and [H+] gradient across membrane (created by electron transport chain) are used to
make and export ATP
•F1F0 ATP synthase allows protons to enter the matrix, driving ATP synthesis
•Aerobic respiration produces about 30 ATP per glucose molecule, versus 2 for anaerobic fermentations
Topic 17

Fed State

•
•
•
•

Blood glucose is high, pancreas secretes insulin
Initially, flux through glycolysis and citric acid cycle is high because of high [substrate] and
[insulin]
Eventually, [ATP] and other energy indicators increase, inhibiting glycolysis and citric acid
cycle
Glycogen synthesis, fatty acid synthesis, pentose phosphate pathway, and biosynthesis are
favoured

MIDTERM
2280A 85 multiple choice questions
SECTION: 002
Unfed State
• Blood glucose is low, pancreas secretes glucagon
• Glucose is produced from glycogen and then gluconeogenesis (from amino acids obtained from
protein degradation)
• Adipocytes release fatty acids from storage, and eventually, liver produces ketone bodies
o Ketone bodies will be released when you are in a starving stage (2-3 months)
o People in this state are lacking in energy because there bodies are in a resting state to
reserve energy
• Biosynthesis is not favoured
• The main source of energy will be glucose and then fatty acids after 72 hours

The brain relies on ketone bodies greatly to
Diabetes
• Insulin response is low or non-existent
• Type 1: Autoimmune destruction of pancreatic cells that produce insulin
o Manifests in childhood
o Nothing can be done to help or prevent this
o Beta cells in pancreas are destroyed this unable to make insulin
• Type 2: Insulin resistance coupled with impaired insulin secretion
o Late onset
o Overweight people who do not exercise are at a greater risk of getting this
o Cells that make insulin are in the body but are not healthy so they are unable to make

•
•
•

•

enough insulin
Glucose doesn’t enter cells efficiently, so cells act as if glucose were low: resembles unfed state
Triacylglycerol degradation and gluconeogenesis are stimulated
Ketone bodies accumulate in blood, acidifying it
o Diabetes patients who are not being treated have stinky breathe because there inside are
very acidic
Leads to dehydration and low blood volume
o Patients with diabetes are very thirsty

Topic 18
DNA
à Carries genetic material
RNA
à Template for producing proteins
à RNA splicing
à Makes up much of ribosome (rRNA)
àCarries amino acids to ribosomes (tRNA)
à Regulation of gene expression (miRNA)
• Made up of ribonucleotides, composed of three parts: a sugar, a nitrogenous base and a
phosphate
• Ribonucleoside has no phosphate but it still contains sugars and a nitrogenous base

• Nitrogenous bases:
1
...
Guanosine (G)
3
...
Thymidine (T)
5

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