AP Bio Enzymes ≽^• ˕ • ྀི≼
Metabolism
set of chemical processes that occur in living organisms to convert food and liquids into energy
divided into two parts
anabolic → stores energy, builds
catabolic → releases energy, breaks down
Catabolic vs anabolic
catabolic reaction
breaks down complex molecules into simpler ones
releases energy
also known as exergonic
also known as degradative pathways
examples: digestion, cellular respiration
anabolic reaction
builds up molecules from simple to large
stores energy
also known as endergonic
also known as biosynthetic passageway
examples: photosynthesis, protein synthesis
Energy
the. capacity to do work
kinetic energy
the energy associated with the motion of objects
can be harnessed to drive biological processes such as enzyme-catalyzed reactions.
potential energy
the stored energy of an object due to its position or arrangement
can be converted to kinetic energy during biochemical reactions
ultimately influences enzyme activity and efficiency.
Law of thermodynamics
1st law
energy cannot be created nor destroyed, only converted from one to another
2nd law
any energy transfer, some energy is lost as heat and total entropy of the system increases, leading to a decrease in usable energy for work.
entropy → disorder of a system and its surrounds always increase overtime
Endergonic vs Exergonic reactions
Endergonic reactions
Require energy input
results in higher energy products than reactants.
These reactions are non-spontaneous and have a positive change in Gibbs free energy (ΔG > 0).
reactions are uphill
absorbs free energy
Exergonic reactions
Releases energy
results in lower energy products than reactants
These reactions are spontaneous and have a negative change in Gibbs free energy (ΔG < 0).
reactions are downhill
can occur with or without added energy
ADP/ATP cycle in energy coupling
ATP is hydrolyzed to ADP
releases energy for cellular work
ADP is rephosphorylated to ATP, storing energy
powered by energy from catabolic reactions like cellular respiration
ensures a steady accessible supply of energy for various cellular functions
Basic structure/function of enzymes
basic structure
protein structure levels
primary structure → codes for enzyme
secondary structure → specific pattern, folds the protein
tertiary → interaction between r - groups, 3 dimensional shape
quaternary structure → multiple polypeptides
active site
a specific pocket/groove on enzyme’s surface where substrate binds
are unique to specific substrate
where the chemical reaction takes place
lowers activation energy to speed it up
can be used again unless denatured
when substrate latches onto enzyme it is an induced fit model
the enzyme itself has -ase at the end of it
basic function
acts a biological catalyst
speeds up chemical reactions by lowering activation energy required for the reaction to start
Relationship between activation energy and enzymes
enzymes lower the activation energy needed for a reaction → allows the reactants to transition to products more efficiently and at a faster rate.
the reactant, product, and change in free energy stay the same
Induced fit model
describes how an enzyme’s active site changes shape upon binding with a substrate to create a tighter, more precise fit
the enzyme’s active site is has a more flexible structure that can adjust its shape to better accommodate the substrate
after substrate detaches it returns to its original shape
Factors that impact enzyme’s rate of reaction
temperature
lower temp
slows down enzyme activity
higher temp
causes denaturation
sharp decrease in function
humans have an optimal temperature around 37 degrees celsius
pH
lower pH
can cause denaturation
in the stomach → it is the optimum pH (2-3)
higher pH
can cause denaturation
the optimum pH is 7 (usually) in humans
Substrate and enzyme concentration on enzyme’s rate of reaction
substrate concentration
lower substrate concentration
reaction rate increases proportionally with the increase in substrate concentration until it reaches a saturation point, beyond which the reaction rate levels off as all enzyme active sites are occupied.
higher substrate concentration
leads to an increase in reaction rate as well, but once the enzyme is saturated, the reaction rate will not improve further. This is known as enzyme saturation and indicates that the maximum reaction capacity of the enzyme has been achieved.
enzyme concentration
lower enzyme concentration
results in a slower reaction rate since fewer active sites are available for substrate binding
higher enzyme concentration
increases the reaction rate, as there are more active sites available, allowing for more substrate molecules to bind simultaneously, ultimately leading to a more efficient catalysis.
Competitive and noncompetitive inhibitors
competitive inhibitor
prevents active enzyme from working by going against/competing with the substrate for binding to the active site, reducing the overall reaction rate.
can be overcome by increasing the concentration of the substrate, which allows more substrate molecules to bind to the active site, thereby increasing the reaction rate despite the presence of the inhibitor.
noncompetitive inhibitor
prevents active enzyme from working by binding to an allosteric site
changes the enzyme’s shape (temporary or permanent depends)
cannot be overcome, lowers the maximum reaction rate → enzyme is less functional
Allosteric site
a regulatory site on the enzyme
where a modulator binds
binds through non covalent interactions
triggers a change in enzyme’s 3 dimensional shape
transmitted to an active site
effect: causes a confrontational change in enzyme → alters shape
allosteric inhibition decreases enzyme activity
allosteric activation increases enzyme activity
Feedback inhibition
a regulatory mechanism in metabolic pathways
where the end product of a pathway inhibits an enzyme that acts earlier in the same pathway
prevents overproduction and conserving cellular resources
example:
glycolysis and ATP
glycolysis is a pathway that breaks down glucose to produce ATP
when cell has a lot of ATP, the ATP molecules bind to the allosteric site of PFK 1
causes PFK 1 to change shape which inhibits activity and slows down glycolysis
similarly, if there is too little ATP, the ATP molecules would drop so glycolysis would speed up again
Pigment
Molecule that absorbs light energy.
Different pigments absorb different wavelengths of light — this allows plants to capture more energy.
Pigments are separated by their polarity and solubility in the solvent.
Chlorophyll a
Main pigment; absorbs violet-blue and red light, reflects green.
located in reaction center of photosynthesis
Chlorophyll b
Accessory pigment; absorbs blue and orange light.
transfers light energy to chlorophyll
Carotenoids
Accessory pigments that absorb blue-green light and protect chlorophyll from damage.
can give off orange, yellow, red colors
Xanthophylls
Yellow pigments that help absorb excess light energy.
Chromatography
Technique that separates molecules based on their solubility and polarity.
Solvent front
The furthest point the solvent travels up the chromatography paper.
Rf value
The ratio of the distance traveled by the pigment to the distance traveled by the solvent.
Formula: Rf = (distance pigment traveled) / (distance solvent traveled)
Polarity
Determines how far pigments move — more nonpolar pigments move farther with the nonpolar solvent.
Photosynthesis
Process by which plants convert light energy into chemical energy (glucose).
Light-dependent reactions
Occur in the thylakoid membrane; convert light energy to chemical energy (ATP + NADPH).
Reduction
Gain of electrons (DPIP becomes colorless).
Oxidation
Loss of electrons.
Spectrophotometer
Measures how much light is absorbed (absorbance) by a solution.
Algae beads:
Contain living photosynthetic cells that both photosynthesize and respire.
Phenol red
pH indicator that changes color based on CO₂ levels.
Yellow = acidic (high CO₂)
Purple = neutral/basic (low CO₂)
Photosynthesis equation
6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂
absorbs CO2 → more basic
CO2 and H2O are taken from atmosphere and soil
converted into glucose
light energy is absorbed by pigments like chlorophyll
glucose is made from CO2 (carbon)
serves as plants’ food source
O2 is released as waste product into the atmosphere when water molecules are split during light dependent reactions
Cellular respiration equation
C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP
releases CO2 → more acidic
Carbon dioxide (CO₂)
Produced in respiration, consumed in photosynthesis.
pH
Measure of hydrogen ion concentration; lower pH = more acidic.
Autotrophic
an organism that creates its own food using light (photosynthesis) or chemical energy (chemosynthesis)
forms the base of food webs as a primary producer
photoautotrophs
organism that produces their own food using sunlight CO2 + water during photosynthesis
usually occurs in chloroplasts for plants and thylakoid membranes for prokaryotes
chemoautotrophs
organisms that create their own organic food from inorganic compounds
uses chemical energy instead of sunlight
Heterotrophic
an organism that cannot produce its own food and must consume other organism for energy and nutrients
also known as consumers
use cellular respiration to convert food into energy
Stomata
tiny pores typically found on lower epidermis that regulate gas exchange and controls rate of transpiration
Vein
forms the transport network within the leaf
contains xylem (transports water and minerals to the mesophyll cell) and phloem (transports the sugar produced during photosynthesis to other parts of the plant)
Mesophyll
the ground tissue of the leaf
located between the upper and lower epidermis
primary site where photosynthesis occurs
cells are packed with chloroplasts
the air spaces in the spongy layer facilitates the diffusion of gases to and from the stomata
Inner Membrane
a selectively permeable membrane that regulates the passage of materials into and out of the stoma
Outer Membrane
a highly permeable membrane that encloses the entire organelle and allows for the passage of small molecules and ions
Thylakoid
disc shaped membrane
membrane contain chlorophyll, electron transport chains, light dependent reactions, which convert light energy into chemical energy (ATP and NADPH)
located in the stroma
multiple thylakoids are called granum/gran
Stroma
fluid inside the inner membrane
surrounding the thylakoiuds
contains enzymes, ribosomes, chloroplast DNA
the light independent reactions of photosynthesis (calvin cycle) occurs here, converting CO2 into sugars
Redox Reaction
a chemical equation where electrons are transferred from 1 atom, ion or molecule to another
can be oxidized → loses electrons
can be reduced → gains electrons
photosynthesis in light dependent reactions, water molecules (H2O) are oxidized, this process releases electrons, protons, and O2, in the calvin cycle, the electrons, protons generated from wter and is used to reduce CO2
Light Reactions (Dependent)
light energy is captured by pigment and used to split water molecules
releases electrons, protons and O2
electrons go to chain that drives ATP and reduces NADP+
occurs in thylakoids memnranes
water + light energy → ATP and NADPH + O2
Intermediate products: ADP, NADP+. H+ and electrons
STEPS
Photosystem 2
water splits, electrons get excited and are transferred to the primary electron acceptor
Electron Transport Chain
ATP is made
transported to Photosystem 1
Photosystem 1
absorbs light energy, which excites electrons and allows them to be transferred to NADP+ to form NADPH
completes the light-dependent reactions of photosynthesis.
Short Electron Transport Chain
makes NADPH reduced to NADP
Calvin Cycle (Light independent reactions)
the ATP and NADPH produced in the light reactions area are used to fuel the cycle in the stroma
occurs in the stroma
CO2 + ATP + NADPH → sugars\
Intermediate Products: G3P, PGA
STEPS
Carbon Fixation
enzyme RuBisCO combines 1 molecule of CO2 with a 5 carbon sugar called RuBP
creates an unstable 6 carbon compound that immediately gets split into 2 molecules of 3 carbon compound called 3 PGA
Reduction
energy from ATP and NADPH are used to to convert 3PGA into G3P
the 3PGA is reduced and phosphorylated to form a G3P molecule
for every 1 turn of cycle one G3P is exported to be used for glucose (3 cycles=1 glucose)
ATP is converted to ADP and NADPH to NADP+ they return to light energy
Regeneration
remaining G3P molecules along with more ATP are rearranged through a series of complex reactions to regenerate RuBP molecules needed for carbon fixation
the product is RuBP (completes cycle), and preparing it to the fix another CO2
Photosystem
a protein-pigment complex in thylakoid membrane that harvests light energy for photosynthesis by funneling it to a reaction center
Electron flow in light reactions
water molecules are split to replace the electrons lost by PS11 → releases electrons, H+ and O2
light energy excites electrons in the reaction center of PS11 (P680) and are then passed to primary electron acceptor
these high energy electrons are passed down an electron transport chain, losing energy along the way
the energy released by the electrons moving through the 1st ETC pumps proteins (H+) from the stroma into thylakoid lumen, creating a proton gradient
the low energy electrons arrive at photosystem 1 and are passed to a molecule called PC which carries them to PSI
light energy is absorbed by pSI, re-excites the electrons to a higher energy level
the high energy electrons are passed to 2nd ETC where they move down to a lower energy state by molecules
the electrons are transferred from molecules
the electrons are transferred from molecule to the enzyme NADP+ reductase, which uses them to reduce NADP+ to NADPH
final products are NADPH and ATP which are used in the calvin cycle
chemiosmosis
the process of creating ATP by using energy from a proton H+ gradient (high to low) to power an enzyme called ATP synthase
used when light reactions occur in the thylakoids
H+ are pumped from stroma into thylakoids plus splitting of water release mole H_ which adds to gradient
H+ flows out of thylakoid and into stroma by protein channel, ATP synthase, the energy released as H+ moves through the protein channels causes ATP to be produced ATP is used for calvin cycle
C3 Plants → normal plants
Initial CO2 fixation enzyme: RuBisCO
Initial Stable product: 3PGA
Location of calvin cycle: mesophyll
Time of Stomata opening: day
Adaptation to environment: moderate climate
C4 Plants → sugar-cane, corn
Initial CO2 fixation enzyme: PEP carboxylate
Initial Stable product: oxalacetate
Location of calvin cycle: fixation: mesophyll, cycle: bundle sheath
Time of Stomata opening: day (partially open)
Adaptation to environment: hot, dry, efficient water use
STEPS
converts to 4 carbon compound
transported to bundle sheath cells
releases high concentration of CO2 for calvin cycle
CAM plants → desert plants, pineapple
Initial CO2 fixation enzyme: PEP carboxylate
Initial Stable product: malic acid
Location of calvin cycle: both processed in mesophyll, but a different times
Time of Stomata opening: night
Adaptation to environment: arid climate, efficient water use
STEPS
at night → opens stomata and absorbs CO2 and stored in vacuoles
during day, closes stomata to conserve water and stored acid is converted back to CO2
C4 and CAM evolution
adapts by water storage in fleshy tissue
extensive root systems
reduced water through modified leaves or spines of waxy cuticles
open stomata at night to conserve water