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Sucrose + Oxygen can be oxidized – or metabolized – into carbon dioxide and water
Sucrose is very stable – this reaction cannot happen spontaneously
A catalyst facilitates the reaction
When this occurs non-biologically (e.g. burning the sucrose) it is simple chemistry
Introduction to Glycolysis
Cells undertake similar processes to derive energy; the oxidation of an energy rich
molecule like
glucose (another sugar) occurs within our cells daily
This is the basic reaction:
In the simple reaction, one glucose molecule is broken down into two pyruvate
molecules with a
net gain of 2ATP (the energy carrying molecule of our cells)
In terms of biochemistry, this process actually takes 10 separate steps, some of which
consume
energy, others of which release energy
Glycolysis -Process Overview
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Now let’s review the high level step by step process for Glycolysis. In the next
section we will be reviewing each of these steps involved in Glycolysis in detail.
Glycolysis -Step 1
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Glycolysis -Step 2
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In this step G6P is rearranged into fructose-6-phosphate (F6P) by glucose phosphate
isomerase (as depicted below)
This isomerization process helps maintain stability of the reaction process
Important Note:
Notice how all the enzyme names have a common format:
End with ase
Name tends to describe it’s function
E.g phosphorylase adds a phosphate
Glycolysis - Step 3
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In another energy-consuming step, F6P is modified into Fructose 1,6 bisphosphate
This is a non-reversible reaction and helps drive the energetics by destabilizing
the molecule
Glycolysis - Step 4
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In the next step, the destabilizing of the molecule in the previous reaction allows the
hexose ring to
be split by aldolase into two triose sugars: dihydroxyacetone phosophate (DHAP) and
glyceraldehyde
3-phosphate (GADP).
Glycolysis - Step 5
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Glycolysis - Step 6
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This begins the “payoff” phase, where energy is produced – the conversion of GADP
to
1,3 bisphosphoglycerate (1,3BPG) results in the net production of an Nicotinamide
Adenine
Dinucleotide Hydrogen (NADH)
Glycolysis -Step 7
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Glycolysis - Step 9
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In this step Enolase now converts 2PG to phosphoenolpyruvate (PEP) as shown
below.
Glycolysis - Step 10
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Glycolysis is only one essential enzymatic process, and as seen it actually requires 10
unique
enzymes.
Another important biological process is fermentation.
Fermentation is a metabolic process that converts sugars to acids, gases, and alcohol.
Occurs in yeast and bacteria, and in oxygen-starved muscle cells, as in the case of
lactic acid
fermentation
Used more broadly to refer to the bulk growth of microorganisms on a growth
medium, often
with the goal of producing a specific chemical product
There are many different types of fermentation, all of which are enzymatic.
Ethanol Fermentation
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Pepsin
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Pepsin is a protease – which as you might guess is an enzyme which can break
down proteins
Pepsin is the primary digestive enzyme in our stomachs
Cleaves peptide bonds primarily between hydrophobic and aromatic amino acids
Important function is collagen digestion
Collagen is the fibrous portion of meats
Pepsin is capable of autolysis – it can cleave itself!
Now let’s review the structure of Pepsin and the hydrolysis of the peptide bond.
Ribozymes
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Ribozymes are “enzymes” – catalytic, biologically active – but comprised of an
RNA which has formed a secondary structure.
RNA can be both genetic material (like DNA) and a biological catalyst (like
protein enzymes)
RNA molecules that are capable of catalyzing specific biochemical reactions,
similar to the action of protein enzymes
Various functions, but primarily involved in RNA/DNA transactions – include in
the ribosome (protein synthesis)
The existence of ribozymes supports the RNA World hypothesis, which suggests
that the first “living” molecule to evolve on the Earth was an RNA
Now let's review a schematic of the Ribozyme cleavage of the RNA.
We have only looked at a few functional enzymes out of the thousands that exist
All of them function using what we suspect is the “lock and key” system first
suggested by Emil
Fisher
The lock represents an enzyme and the key represents the substrate it acts upon
Both enzyme and substrate have fixed, complementary conformations that lead to a
fit
At the active sites, the enzyme has a specific geometric shape and orientation that a
complementary substrate fits into perfectly
A more modern understanding suggests that the induced fit model is more
appropriate – enzymes and substrates are flexible and constantly in
motion – vibrating – and their proximity can induce the correct fit, provided they
are a match. Now let’s review the schematics of the Lock and Key Analogy as
shown below.
PART 2
Introduction
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While enzyme names tend to be named for the substrate and reaction, this can
become unwieldy
So enzymes are additionally classified by their function using what is called an EC
code
The Enzyme Commission (EC) is a body of experts affiliated with the International
Union for
Biochemistry and Molecular Biology (IUBMB)
An EC contains 4 codes separated by periods (e.g. 1.2.3.4) where the first number
designates the
class of reaction performed by the enzyme
Top Level EC Codes
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The following is the list of the top level EC Codes and their 6 classes of enzymes.
EC Specifiers
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Each level of the EC code adds specificity:
EC 3.4 are hydrolases that act on peptide bonds
EC 3.4.11 are those hydrolases that cleave off the amino-terminal amino acid from
a polypeptide
EC 3.4.11.4 are those that cleave off the amino-terminal end from a tripeptide
Important Note:
Each unique enzymatic function, therefore, has a unique EC code.
Structural Proteins
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In addition to catalytic proteins, there are proteins that serves a structural function
Some of these are involved inside the cell, e.g. cell skeleton proteins
Others exist outside the cell
Cell/tissue binding
Communications & Signaling
Extra-Cellular Matrix
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Elastin, as you may expect, forms elastic fibers, allowing tissue to elastically give to
pulling forces
and return to their original shape once the forces relent
This is a key characteristic of arteries, which need to expand and contract with blood
flow pressure
changes caused by the heart’s normal pumping behavior.
750 amino acids in length, elastin is 5 times as stretchable as an equal sized rubber
band.
Elastin is comprised of alternating hydrophilic and hydrophobic regions, which form
fluctuating
beta structures
Elastin is secreted into the folds in the cell surface and their forms fibers via cross-
linking between
lysine residues
Cell Skeleton Proteins
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Many structural proteins serve to provide structure to the internals of the cell:
Microfilaments
Microtubules
Intermediate Filaments
These stabilize the shape of the cell as well as link internal cell structures
Actin Polymerization
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Actin is a highly abundant (10-100 micromolar on average),~42 kDa structural
protein found in all eukaryotic cells (except for nematode sperm)
With more than 95% conservation in the primary structure, actin is one of the most
highly-conserved proteins [1]
The globular form of actin, known as G-actin, forms the basic unit for actin
filaments
In many cases actin filaments may bundle together with other actin filaments, or,
together with their associated motor proteins (e.g. myosin superfamily) form an
elaborate network known as the actin cytoskeleton
This occurs primarily at or near the plasma membrane
Actin filaments are highly dynamic and their polymerization is usually correlated
to their disassembly. Generally, actin filament polymerization occurs over three
phases:
Nucleation phase
Elongation phase
Steady state phase
Because IF proteins are very cell-type specific, they can be used to identify the source
of metastatic tumours
During mitosis, IFs are depolymerized; they repolymerize after division is complete.
Several other proteins have been found to bind IF proteins; these are called
Intermediate Filament Associated Proteins, or IFAPs
Plectin: crosslinks IF to microtubules and the lamin network in the nculeus
Ankyrin: connects IF to plasma membrane proteins and microtubules
PART 3
Introduction
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Many diseases are caused by mutations in enzymes. These can be the result of an
error at any level of the process of making a protein, including:
DNA sequence mutation
Regulatory errors
RNA transcription errors
mRNA translation errors
Protein folding errors
Sequence Mutations
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From the previous course, you should be aware that each codon (set of 3 bases) in the
DNA
sequence for a protein coding gene corresponds to a specific amino acid
Changes in the sequence can result in a change to the amino acid coded for in that
position; even
worse, the resulting codon may code for a STOP signal
Alternately, the deletion or insertion of bases in the DNA can result
in frameshift mutations
Now let's review the Sequence Mutations table listed below that highlights the
sequence mutations
at the first, second and third positions.
Regulatory & Transcription Errors
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A regulatory error can occur in several places
Transcription control: e.g. the “wrong” amount of transcript produced, e.g. not
enough, or too much
Translation control: a shorter polyA tail, for example, will cause the mRNA to
degrade faster
Transcriptional errors can be caused if the RNApolymerase “misreads” the DNA,
inserting an
incorrect base into the RNA
RNApol-II has an error checking function
Error rate is approximately 2 x 10-6, or 2 errors in every million bases
DNA polymerases adds nucleotides to the 3' end of a strand of DNA. If a mismatch is
accidentally incorporated, the polymerase is inhibited from further extension.
Proofreading
removes the mismatched nucleotide and extension continues as shown in the DNA
Polymerase chart below.
Splicing & Translation Errors
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Splicing Errors:
Recall that some genes have alternative splicing
sites
Translation Errors:
Translation errors are even less common: approximately 1 x 10-5, or 1 in
100,000 amino acids
But – this error rate results in 1 in 100,000 amino acids being wrong
An error rate of 1 x 10-6 in transcription, (i.e. 1 in 1,000,000 amino acids), may result
in fewer amino acid changes, depending on where the errors occur!
Protein Folding Errors
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As previously discussed, folding is not simply a matter of finding the lowest free
energy
Chaperones and chaperonins can bind the nascent amino acid chain and modify
which
residues are available to bind
The nascent amino acid chain begins folding while it is still being synthesized – so
the parts of
the chain that have already been translated may bind to themselves, making those
regions
unavailable to as-yet untranslated regions
Chaperones/chaperonins can prevent this preliminary folding, or modify folding in
other
ways
Let’s review the following schematic related to Protein Folding.
Protein Folding Errors (cont'd)
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There are diseases that result from protein misfolding:
Protein folding errors are almost always due to an underlying sequence error in the
protein,
or in the chaperone/chaperonins involved in folding
There are cases where there is no sequence error – the reason for misfolding is
less clearly understood in cases such asthese