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Proteins I and Proteins II - Coggle Diagram
Proteins I and Proteins II
Proteins I - Structure + Function
Amino acids
Structure:
i. have
amino group (-NH2)
,
carboxyl (-COOH)
,
hydrogen atom (-H)
bonded to central 𝛼-carbon
ii. distinctive
R-group
Properties:
i.
Amphoteric
contain
acidic group
(donate H+) and
basic group
(accept H+)
exist as
zwitterions
:
equal
number of
positively
and
negatively charged
functional groups
ii. act as
pH buffers
by accepting or donating H+
iii.
Different reactivity
due to functional groups
functional groups such as carboxyl (-COOH), sulfhydryl (-SH), hydroxyl (-OH), or amino (-NH2) participate in chemical reactions
iv.
Different solubility
due to polarity of side chains
non-polar side chains lack charged / highly electronegative atoms to form hydrogen bonds with water -> hydrophobic
polar side chains interact readily with water -> hydrophilic
Effect of pH
->
disrupt ionic interactions and hydrogen bonding between side chains
-> decreasing pH, increase H+ concentration,
H+
combine with
-COO-
side chains to form
-COOH
-> increasing pH, increase OH- concentration,
OH-
removes H+ from
-NH3+
, form
-NH2
a. Peptide Backbone
Formed:
condensation
reactions between
carboxyl group
of amino acid and
amino group
of second amino acid
Break:
Hydrolysis
End of peptide sequence =
N terminus
Other end =
C terminus
Flexible: single bonds can rotate -> allow peptide chain to fold into different shapes
Effect of temperature
-> Increase temp
-> increase
kinetic energy, vibrate faster
->
disrupt interactions
in secondary and tertiary structure
-> non-polar side chains becomes
exposed to aqueous environment
-> causes them to
aggregate randomly
with other polypeptide,
irreversible change to protein structure
Primary structure
Sequence of amino acids in a polypeptide
Bond:
covalent bonding
(ie. peptide bond)
affects secondary, tertiary and quaternary structure of protein
affects the stability of the -helix as interactions between side chains can stabilise or destabilise helical structure
Secondary Structure
Formation of 𝛼-helixes and 𝛽-pleated sheets in a polypeptide
Bond:
hydrogen bonding
between
oxygen on C=O
and
hydrogen on N-H
ii.𝛽-pleated sheet
folding of polypeptide chain
C=O group of one residue is hydrogen bonded to N-h group on another residue on a neighbouring chain
Antiparallel: neighbouring hydrogen polypeptide chain run in opposite direction
Parallel: neighbouring hydrogen polypeptide chain run in same direction
Tertiary structure
Overall 3D shape of polypeptide
Bonds: hydrogen bonds, hydrophobic interactions, ionic interactions, Van der Waals interactions, disulfide bonds between side chains - between R groups
Quaternary Structure
Shape produced by combinations of polypeptides, consisting of
more than one polypeptide chain
i. 𝛼-helix
twisting of polypeptide chain
-> bring R groups close together, either attract (stabilise) or repel (destabilise)
-> determine whether secondary structure will hold
C=O group of one residue is hydrogen bonded to N-H group four residues
Haemoglobin
1. Compact globular structure
-> allow for
many haemoglobin molecules
to
packed into red blood cells
to carry oxygen
Structure
i.
globular protein with quaternary structure
ii. Consists of 4 subunits:
two 𝛼-chains, two 𝛽-chains
ii. Each subunit binds a single haem group non-covalently
2. Heterocyclic ring structure with a centrally-bound Fe (II) atom
-> allows
oxygen
to be
transported efficiently in blood
3. Quaternary structure
-> binding of oxygen at one haem grp in one subunit
-> trigger
conformational change
to globin chain
-> triggers conformational change in other subunits
->
more oxygen bind to haemoglobin tetramer
, accumulated conformation change causes quaternary to be stable
->
increase oxygen affinity
-> enables haemoglobin to be saturated with oxygen at high partial pressure of oxygen, release oxygen at low partial pressure of oxygen in respiring tissues
Collagen
Structure + Function
1. Basic triple helix structure - tropocollagen
3 collagen polypeptide chains
high content of glycine, hydroxyproline and hydroxylysine
high content of glycine, proline and hydroxyproline
-> cluster in the middle
-> obstruct formation of hydrogen bonds
-> prevents collagen polypeptide from forming 𝛼-helix
i. Staggered structure
-> stabilised by hydrogen bonds
-> bulky and relatively inflexible proline and hydroxyproline residues confer rigidity
-> create tensile strength of collagen
ii. Organised into staggered arrays to form strong fibrils
-> covalent cross linking between tropocollagen molecules occur near N and C termini, involving hydroxylysine and lysine residue
-> makes collagen insoluble insolvents that disrupt hydrogen bonding and ionic interactions
rigid, inextensible fibrous protein
G protein
Cell signalling
-> bind to a signal molecule on the extracellular domain
-> bring conformational change in the cytoplasmic domain
-> triggers a signal cascade in the cytoplasm
Structure:
i. Seven transmembrane 𝛼-helices
stably anchored in the hydrophobic core of the plasma membrane by the many hydrophobic amino acids on the outer surface of the seven membrane-spanning segments
ii. Binding site for ligand and G-protein
Ligands - extracellular side
G proteins - cytosolic side
Proteins II - Enzyme
Effect of
Enzyme concentration
Low enzyme concentration, add more enzyme
-> increase enzyme concentration
-> increase
rate of effective collision
between enzyme and substrate molecules
->
more enzyme-substrate complex are formed
->
rate of reaction increases
High enzyme concentration
-> enzyme concentration
no longer limiting factor
-> substrate concentration must increase, rate of reaction increase
Effect of
Substrate concentration
-> increase in substrate concentration, increase rate of reaction
-> but at Vmax,
enzyme molecules are saturated, sunstrate molecule need to wait until enzyme substrate complex has released products
substrate becomes limiting factor
Effect of
pH
At optimum pH:
-> R-groups of amino acid have appropriate charges
-> 3D conformation allows enzyme to function effectively
->
rate of effective collision
between enzyme and substrate molecule to form enzyme-substrate complex is at the
highest
->
large
amt of
products formed
->
rate of reaction is at maximum
Slight deviation to pH
->
alter charges
of acidic and basic R-groups of amino acids of enzyme
-> reduces ability of substrate to bind to active site
-> rate of formation of enzyme substrate complex decrease
->
rate of reaction decreases
Drastic change to pH:
-> disrupt ionic bonds and hydrogen bonds that maintain 3D structure of enzyme
-> structure of enzyme distorted, no longer complementary to substrate
-> substrate can no longer bind to active site to form enzyme substrate complex
-> enzyme denatured
-> rate of reaction decreases drastically
Mode of Action
1. Active sites
i. binds the substrates
-3D cleft formed by amino acids
ii. takes up small part of the total volume enzyme
iii. unique microenvironment
iv. Substrates are bound to enzymes by multiple weak attractions
v. Specify of binding depends on the precisely defines arrangement of atoms in an active site
3. Lowers Activation Energy
i. maintain precise substrate orientation
ii. change substrate reactivity by altering elestrostatic structure
iii. exert physical stress on bonds in the substrate to be broken
4. Show substrate specificity
i. Absolute specificity
catalyse only one reaction (eg. catalase)
ii. Group specificity
act only on molecules that have specific functional group, such as hydroxyl, amino, phosphate group (eg. carboxypeptidase)
iii. Linkage specificity
act on a particular type of chemical bond (eg. phosphatases)
iv. Stereochemistry specificity
act on particular stereoisomer
2. Forms enzyme substrate complex
Catalytic cycle of Enzyme
Substrate
collide with
active site
of the enzyme with correct orientation and with energy higher than or equal to Ea
Lock and Key Hypothesis:
substrate bind to enzyme active site that is
complementary in structure
and charge
form enzyme substrate complex
Induced - Fit Hypothesis:
substrate bind to active site
cause
conformational change
so that active site is complementary to substrate
form enzyme substrate complex
Substrate
interact with catalytic residue
in active site through weak interactions
Enzymes lower Ea to facilitate
formation of unstable transition state
Lower Ea
increase formation of products
Transition state converts to products, form
enzyme substrate complex
Product
released
from active site
Effect of
Temperature
Low Temp: rate of reaction is 0 / low
->
kinetic energy
of enzyme and substrate molecule is very
low
->
rate of effective collision
between enzyme and substrate molecule is
low
->
enzymes
are
inactive
Temp rises to optimum temp
-> temp increases
->
kinetic energy
of enzyme and substrate molecules
increases
->
rate of effective collision
between enzyme and substrate molecule
increases
->
more enzyme-substrate complexes
form
->
more product molecules
form
->
rate of reaction increases
At optimum temp:
->
rate of effective collision
between enzyme and substrate molecule to form enzyme-substrate complex is at the
highest
->
large
amount of
product molecules
formed
Beyond optimum temp:
->
kinetic energy
of enzyme and substrate complex continues to
increase
with temperature
->
higher frequency of collision
-> but rise in temp cause
thermal agitation
,
disrupt weak bonds
that maintain the tertiary and secondary structure
-> 3D structure of active site
distorted,
no longer complementary in shape
and charge to substrate
-> substrate molecule
cannot bind
to enzyme molecule to form enzyme substrate complex
-> enzyme denatured
->
rate of reaction decreases
Enzyme Inhibition
Non-competitive inhibitor
-> binds to
enzyme active site
-> active site functions less effectively
->
prevents formation of products
Competitive inhibitor
->
resembles
the substrate and
binds
to the active site
->
prevents
substrate from binding
->
reduces concentration of free enzyme
available for substrate binding
Solution:
Increase substrate concentration
->
higher probability
of substrates forming enzyme substrate complex
Allosteric regulation
Allosteric activator
-> stabilises enzyme in active form
->
promotes
binding
Allosteric inhibitor
-> stabilises enzyme in inactive form
->
prevents
binding of substrate to active site