Energy and Enzymes Flashcards
Based on Carbon source:
Autotrophs – CO2 only
Heterotrophs – organic forms of carbon (e.g. glucose)
Based on Energy source:
Phototrophs – use sunlight (photosynthetic organisms)
Chemotrophs – use organic compounds (e.g. glucose) or inorganic
compounds (e.g. iron, sulphur)
Metabolism
- The sum of all the chemical reactions that occur within a cell/organism
- Structured into metabolic pathways
- Complex molecules broken down into simpler compounds (CATABOLISM)
Energy released - Simple molecules used to construct complex compounds (ANABOLISM)
Energy utilised - Metabolism = management of cellular material and energy
Free energy and equilibrium
- In spontaneous reactions, the free energy of the system decreases (G < 0)
➢ EXERGONIC - Non-spontaneous reactions require the input of free energy (G > 0)
➢ ENDERGONIC - For a reaction at equilibrium, G= 0
➢ To remain alive cells must maintain disequilibrium
→ product of one reaction becomes the reactant in the next step
➢ Evolution of a metabolic pathway - Exergonic processes drive endergonic reactions
➢ ENERGY COUPLING – key molecule is Adenosine Triphosphate (ATP)
ATP
- Synthesis of cellular macromolecules (DNA,
protein, polysaccharides) - Synthesis of other cellular constituents (e.g.
membrane phospholipids) - Cellular movement
- Transport of molecules against a
concentration gradient - Electrical energy
- Temperature maintenance
Reaction △G (kcal/mol)
ATP + H2O → ADP + Pi
-7.3
In an exergonic reaction, energy is
released to the surroundings
ADP + Pi → ATP + H2O
In an endergonic reaction, energy is
absorbed from the surroundings
+7.3
Photosynthesis:
6CO2 + 6H2O → glucose + 6O2 +686
What are enzymes
▪Biological catalysts
▪Usually globular proteins
▪Substrate binds and converts to product at active site
▪Enzymes can increase the rate
of a reaction by up to 1020
▪Lower activation energy
Cofactors & Coenzymes
Cofactors
▪Inorganic substances bound to active site (zinc, potassium, iron, magnesium etc.)
Coenzymes
▪Assist enzymes by accepting and donating
H+ and e-
▪Organic molecules often derived from
vitamins (NAD+, FAD, NADP+
Prosthetic Group
▪Tightly bound
▪Specific non-polypeptide unit in
a protein
▪Determines/involved in enzymes
biological activity
Enzyme structure
Primary structure
▪Chain of amino acids joined
together with peptide bonds
▪Amino Acids = -NH2 (Amine)
+ -COOH (carboxyl) + R group
side chain
Secondary Structure
▪Hydrogen bonds between H from
NH2 and O from COOH
▪Results in chain folding in either
α-helix or β-pleated sheet
Tertiary Structure
▪3D structure, further folding
▪Primarily due to interactions between the R groups of the amino acids
▪R groups with like charges repel one another,
while those with opposite charges can form an ionic bond
▪Disulfide bonds = covalent linkages between the sulfur-containing side chains of cysteines - stronger than the other types of bonds that
contribute to tertiary structure
Quaternary Structure
▪Assembly of more than one
polypeptide chain
▪E.g. DNA polymerase, haemoglobin
Lock & Key Model (1894)
▪ Assumes a high degree of similarity
between the shape of enzyme and
substrate
▪ 3D jigsaw puzzle
▪ Does not take into account
conformational flexibility
▪ e.g. Chymotrypsin
Induced Fit Model (1958)
▪Binding of substrate induces a
conformational change in the
enzyme that results in a
complimentary fit after the
substrate is bound
▪e.g. carboxypeptidase
EC Number
EC number = Enzyme
commission number
Suffix –ase
Effect of Substrate Concentration
▪ Increasing substrate concentration
▪ Increases the rate of reaction
(enzyme concentration is constant)
▪ Maximum activity reached when
all of enzyme combines with
substrate
Effect of Temperature
▪Little activity at low temperature
▪Rate increases with temperature
▪Most active at optimum
temperatures (usually 37°C in
humans)
▪Activity lost with denaturation at
high temperatures
Effect of pH
▪Each enzyme has an optimum pH
▪Many enzymes have an optimum of
~6.8
▪Deviations from optimum can lead
to changes in ionisation of groups at
the active site and eventually
enzyme denaturation
Zero Order Reaction
▪Rate of reaction is independent of substrate
concentration
▪Seen when catalyst is saturated
▪Rate of the reaction is equal to k
First Order Reactions
▪Rate of reaction is proportional to the
frequency in which the reacting molecules
come together
▪A -> P
▪ 𝑣 = 𝑑[𝑃]/𝑑𝑡 = − 𝑑 [𝐴] /𝑑𝑡 = 𝑘[𝐴]
Second Order Reactions
▪Bimolecular reactions
▪2A -> P
▪𝑣 = − 𝑑 [𝐴/]𝑑𝑡 = 𝑘[𝐴]62
▪A + B -> P
▪𝑣 = − 𝑑[𝐴]/𝑑𝑡 = − 𝑑 [𝐵]/𝑑𝑡 = 𝑘[𝐴][𝐵]
Michaelis Menten Kinetics
The Michaelis-Menten
equation describes the
initial reaction rate of a
single substrate with an
enzyme under steady state
conditions
𝐾𝑀 = 𝑘−1 + 𝑘2/ 𝑘1
k1 = formation of the enzyme-substrate complex
k-1 = the reverse reaction
k2 = formation of a product and dissociation from the enzyme
𝑣𝑜 = 𝑉𝑚𝑎𝑥[𝑆]/𝐾𝑀 + 𝑆
Units
Km = substrate con centration such as μM or mM
Vmax = amount substrate converted/time
Turnover Number Kcat
▪Kcat describes the number of reactions (turnovers) at each active site in a given time
▪Kcat = Vmax/[E]T where [E]T = [E] + [ES]
▪Turnover numbers can only be calculated when the concentration of enzyme is known
▪Vmax can be calculated by rearranging this equation
▪Specific activity = units of activity per mg of protein
▪Kcat/Km = Measure of catalytic efficiency
Regulation of Enzyme activity – Allosteric Control
Binding at a site other than the active site, which enhances or inhibits the activity of the active site
Allosteric enzymes = multi-subunit proteins with an active site on each subunit, which cooperatively bind
substrate molecules such that the binding of substrate at one active site
induces a conformational change in the enzyme which alters the affinity of the
other active sites for substrate
Reversible covalent modification = e.g.
phosphorylation
Regulation of Enzyme activity – Feedback Inhibition
End-product feedback
inhibits the committed step earlier in the pathway to prevent the build up of
intermediates and waste metabolites and energy
Competitive Inhibition
Compete with the substrate to
occupy the active site.
Inhibitors tend to have a similar
structure to the substrate.
𝐾𝐼 = 𝐸 [𝐼]/[𝐸𝐼]
