Please enable JavaScript.
Coggle requires JavaScript to display documents.
Week 2 Lecture 5: Proteins and Enzymes (Enzymes (Specificity (Enzyme for…
Week 2 Lecture 5: Proteins and Enzymes
Functions
Hardware
Interpret DNA
Enzymes
Accelerate and regulate reactions, as catalysts
Structure and movement
Cytoskeleton and connective tissues
Motor proteins, are mechanochemical enzymes
Regulation
Hormones
e.g. insulin, a protein hormone
Defence
Amino acids
20 in total, that life uses
Building blocks of protein
Structure
4 groups
bonded to a central α-carbon atom
These four groups include...
Amino group (NH3+)
Side chain (R)
Serves to differentiate between different amino acids
In different shapes and sizes
Some are polar but uncharged
Hydrophilic (i.e. dissolves in H2O)
#
Some are charged
ALSO hydrophilic
Some are non-polar
Hydrophobic
Some form rings
Some have special properties
Cysteine links two amino acids by forming disulphide bonds (S–S) – i.e. a sulfhydryl group (–SH) covalently bonds to another sulfhydryl group
Hydrogen atom
Carboxyl group (COO-)
Types
Amino acids with electrically charged side chains
Positive
Arginine
Histidine
Lysine
Negative
Aspartic acid
Glutamic acid
Amino acids with polar
but
uncharged side chains (dissolve in aqueous solutions)
Serine
Threonine
Glutamine
Asparagine
Special cases
Cysteine
Glycine
Proline
Amino acids with hydrophobic side chains (non-polar environment)
Alanine
Lsoleucine
Methionine
Tryptophan
Phenylalanine
Valine
Leucine
Tyrosine
Proteins
Formed by condensation polymerisation reaction of amino acids (the monomers)
When the amino and carboxyl groups of two amino acids react to form a peptide bond, a molecules of water is lost as each linkage forms
A polymer of amino acids is known as a
polypeptide
Each amino acid is joined to another via
peptide bonds
The chain of amino acids is always LINEAR (never branched)
Each subsequent amino acid is always joined from the RIGHT HAND end
Amino acids are always joined from the carboxyl end and read from left to right
This also correlates to the direction of protein translation
When a protein is translated from mRNA, it is created from the N to C terminus
Different lengths and orders of amino acids give rise to almost infinite permutations for polypeptides
Polypeptide terminals
N terminus (+H3N)
Refers to the free amino group that starts a protein or polypeptide
C terminus (COO-)
Refers to the free carboxyl group that terminate a protein or polypeptide
Synthesised by
ribosomes
Ribosomes are found in ALL cells
Facet of the 'Unity of biochemical processes'
All organisms perform the central dogma of molecular biology
DNA –> RNA –> protein
This means that the 1st organism ever to exist (a cell) had this system as well
Structure
Made of two subunits, joined together
A large subunit
A small subunit
mRNA and the newly synthesised peptide run through and between the protein subunits
Protein structure/levels
1.
Primary structure
The
sequence
of amino acids held together by peptide bonds
Read from left to right
2.
Secondary structure
Conformational change in primary structures, causes by the formation of weak
electrostatic and hydrogen bonds
between nearby amino acids
Hydrogen bonding between the δ+ hydrogen of a –NH group in one peptide link and the δ- oxygen of the polar –C=O group in another peptide link
at regular intervals
These forces
coil
and
pleat
the protein molecule, forming two types of secondary structure
α-helix
β-pleated sheet
However, some proteins are
unstructured
3.
Tertiary structure
The ultimate configuration that a polypeptide chain takes in reaching the configuration of
minimal free energy
Bending of the polypeptide chain at specific sites to produce the macromolecule's
3D structure
The tertiary structure includes a buried interior and a surface exposed to the outside environment
These outer surfaces interact with other macromolecules in the cell
This is done so via the
interactions between the R groups
of different amino acids in a polypeptide chain
This includes...
Covalent disulphide bridges
Two cysteine molecules in a polypeptide chain can form a disulfide bridge (–S–S–) by oxidation (removal of H atoms)
Hydrogen bonding
Occurs between side chains, to stabilise folds in proteins
Van der Waals forces
Helps to stabilise close interactions between
hydrophobic
side chains – they aggregate together inside the protein, away from water, and fold as a result
Ionic interactions
Positively charged and negatively charged R groups on different amino acids can form salt bridges
e.g. glutamic acid and arginine
4.
Quaternary structure
Association of the individual polypeptide chains in proteins composed of
multiple polypeptides
How individual subunits bind together and interact with each other
Most functional proteins have
two or more
subunits
All the interactions from the tertiary structure are used to establish quaternary structure.
However, protein structure can change slightly
Haemoglobin
(tetramer – four subunits)
The weak nature of hydrophobic interactions, van der Waals forces, hydrogen bonding and ionic interactions, permits small changes in the quaternary structure
This change aid the protein’s function – which is to carry oxygen in red blood cells
As hemoglobin binds one O2 molecule, the four subunits shift their relative positions slightly, changing the quaternary structure
1 more item...
Protein denaturation
Denaturation disrupts the tertiary and secondary structure (weak electrostatic non-covalent interactions)
This can be done via...
Increasing temperature
Increased molecular kinetic energy, which breaks hydrogen bonds and hydrophobic interactions
Changes in pH
Ionic attractions and repulsions can be disrupted between carboxyl and amino groups in the R groups
Having high concentration of polar substances
Can disrupt hydrogen bonding
Having high concentration of non-polar substances
This coupled with an abundance of hydrophobic interactions disrupts the protein structure
Therefore, it is important to keep the native protein in neutral pH and a neutral environment
Denaturation usually destroys the protein's biological functions
However
,
renaturation
(reassembly of a protein into its native, functional state) is sometimes possible, provided you do not use heat to disrupt the primary structure – instead you
use chemicals
The primary structure specifies how a protein assumes its tertiary structure
Different molecular representation models
(esp. for proteins)
Space-filling model
Allows one to see how other molecules
interact with specific sites and R groups
on the protein’s surface
Stick model
Emphasizes the sites where
bends occur
, resulting in folds in the polypeptide chain
Ribbon model
Most widely used
Shows the different types of secondary structure and
how they fold
into the tertiary structure
Enzymes
Catalysts
Typically proteins
But some RNA molecules have enzyme activity
Increase reaction rate
#
This is IMPORTANT as if the reactions needed to sustain life did not have enzymes, the reaction would be too
slow
to sustain life
Done so via decreasing Ea
Do not alter final equilibrium (only rate)
Do not alter ∆G
∆G is NOT affected by Ea
The energy needed to place the reactants into a transition-state intermediate is recovered during an exergonic reaction, when the free energy of the reactants are decreasing
Recyclable – not used up
Decrease Ea (activation energy)
Why cannot we add heat to living systems to increase reaction rate?
If we did, all reactions would be accelerated, including destructive reactions such as protein denaturation/
It is therefore better to lower Ea to bring the reactants closer together
This is achieved through
enzymes
and
ribozymes
The Ea must be overcome for a reaction to commence – without a catalyst, it might take a long time for a reaction to overcome it
With a catalyst, the Ea decreases, causing the reactants to assume an alternative transition state with lower free energy – this is much more efficient
The Ea is the amount of
free energy
required to bring the reactants to a reactive transition state
Regulated
They accelerate reactions but also regulate
Specificity
Enzyme for almost every cellular reaction
~10,000 different enzymes in an animal cell
Multiple copies of each enzyme
The probability of a reaction increases with the right fit and orientation of a substrate
Two different models for enzymatic action
'Lock and key'
The substrate molecule fits into the enzyme's active site like a key in a lock, forming an
enzyme-substrate complex
, allowing the enzymes to break the bonds in the substrate and yield the product
Substrate
: The reactant molecule that binds with the active site
The enzyme is now available to catalyse another reaction
The shape of the substrate molecule must
match
the shape of the active site. Non-substrate shape does not fit the active site
Active site
: the specific part of the enzyme molecule that allows interaction with a reactant
Induced fit
The enzyme has flexible structures, and the active site can be modified markedly by the binding of a substrate, forming weak intermolecular interactions with it
Reactive side chains
(R groups – from tertiary structure)
from the enzyme's active site are brought into
alignment with the substrate
, prompting interactions and catalytic mechanisms
The flexible active site moulds itself to achieve a better fit for substrate molecules
After the reaction, the products are related from the active site and the active site
returns to its initial shape
How do enzymes work? (How do enzymes cause the substrate to enter their transition state?)
Orient substrates
When there are two or more substrates,
specific atoms have to be bought together (bonded) in a certain way upon collision
, so that the active site has the right shape to accomodate the substrates
Induce strain in the substrate
Once a substrate has bound to its active site, an enzyme can cause bonds in the substrate to
stretch
, putting it in an
un- stable transition state
Temporarily add chemical groups to the substrates
The side chains (R groups) of an enzyme’s amino acids can make its substrates more chemically reactive, by
changing electric charge on the substrate
Acid-base catalysis
Acidic or basic side chains of the amino acids in the active site transfer H+ to or from the substrate
This destabilises a covalent bond in the substrate, permitting it to break
Covalent catalysis
A functional group in a side chain forms a temporary covalent bond with a portion of the substrate.
Metal-ion catalysis
Cu, Fe and Mn, bounded to an enzyme's R groups, can be oxidised or reduced without detaching from the enzyme.
Transfer of electrons
as catalytic action
Regulation
– slows or increases enzymatic activity
Inhibitors
Competitive
Binds to the active site (there is only one), preventing substrate binding
Significantly
decreases enzymatic catalysis rate
However, if the substrate concentration is increased, the substrate is more likely to bind and the enzyme is
active
again
The binding is
reversible
, and the
Non-competitive
Binds at a site
other than
the active site, inducing
change in enzyme structure/shape
so that normal substrate binding cannot occur
#
The substrate no longer fits
The change in shape alters the affinity of the active site for the substrate, and so the rate of the reaction is changed
The binding is
reversible
Uncompetitive
Binds after the substrate binds to the enzyme
A binding is therefore created by the uncompetitive inhibitor, binding and
preventing the release of products
Unlike competitive inhibition, uncompetitive inhibition CANNOT be overcome by adding more substrate because the inhibitor and substrate do not compete for the same active site
The binding is
reversible
, allowing some product formation
Uncompetitive inhibitors
decrease
enzymatic catalysis rate
Allosteric regulation
An example of
non-competitive inhibition
Effectors
are used to influence which form an enzyme takes
Allosteric activators/cooperativity (positive modulators)
Stablises
active form
of an enzyme, making binding of a substrate molecule
more likely
Product formation
Allosteric inhibitors (negative modulators)
Stabilises
inactive form
of an enzyme, making it
less likely
to convert to the active form
No product formation
They bind
reversibly
An inhibitor can leave the enzyme
The enzyme can continue to toggle between the two conformations
Substrate molecules can fit back into the active site when the enzyme toggles back to its active form
Feedback loops
In a metabolic pathway, once the first reaction, or the
commitment step
is initiated, subsequent reactions are catalysed to form reaction intermediates
If there is excess amounts of end product, the product itself
allosterically inhibits
the commitment step enzyme
This effectively shuts down the metabolic pathway temporarily
Enzymes for particular pathways are often
physically linked
on membranes
This is called
substrate channelling
When a product is produced, it becomes the substrate, and so forth
Several enzymes are placed in a line
This increases the efficiency of a reaction
Enzyme partners
Some enzymes require other molecules in order to function
Many enzymes require the presence of
non-protein chemical partners
to fulfil the enzyme
Prosthetic groups
Non-amino acid atoms or molecular groupings
Permanently bound to their enzymes
Heme
Binds ions, O2 and electrons
FAD
Carries electrons/protons
Retinal
Converts light energy
Inorganic cofactors
Some
metal ions
are temporary electron holders – helps with redox reactions
Copper (Cu+ or Cu2+)
Oxidation/reduction
Zinc (Zn2+)
Stabilises DNA binding structure
Iron (Fe2+ or Fe3+)
Oxidation/reduction
Coenzymes
Biotin
Carries –COO-
Coenzyme A
Carries –CO–CH3
NAD
Carries electrons/protons
Temporary electron holder
ATP
Provides/extracts energy
Some coenzymes are produced from vitamins
These must be obtained from food (diet) because they cannot be synthesized by the body
Vitamin B3 (niacin)
Used to make the coenzyme NAD (nicotinamide adenine dinucleotide)
Vitamin C (ascorbic acid)
Helps synthesise collagen, a connective tissue
Vitamin C deficiency causes
scurvy