Biology Unit 3 Aos2

Enzymes

proteins that act as biological catalysts that speed up biochemical reactions by reducing the activation energy required

activation energy

the amount of energy needed to break the bonds of reactant for the reaction to begin

what happens to enzymes during a reaction

enzymes are not consumed during a reaction so they can catalyse many reactions

enzymes can only catalyse reactions when in active form

catalysts

speed up reactions by influencing the stability of bonds in the reactants

Substrate

the compound on which an active enzyme acts as a reactant for an enzyme controlled reaction.

active site

a specific region on the enzyme where the substrate binds, usually a a cleft at the surface

• an enzyme may have more than one active site

active site shape

the substrate matches the shape of an active site, but complementary r groups are also important, such as opposite charges

substrate specific

enzymes are usually substrate specific meaning they will only act on one substrate. However some enzymes do have different active sites, so can act on more than one substrate

lock and key model

proposes that the substrate (s) and the active site fit perfectly

induced fit model

an alternative to the lock and key model that proposes that enzymes and substrates bind at non quite matching sites.

• this affects the stability of the bonds, enabling them to break so that new molecules can be formed

• weak bonds form and induce structural changes in the active site distorting the substrate (s) so that the active site is matched

• the shape of the active site changes slightly to allow a better fit

anabolic reactions

building larger macromolecules or polymers from smaller units called monomers

how anabolic reactions work

• enzyme aligns the substrate to lower the activation energy

• chemical bonds are formed as an input of energy is needed

• e.g. photosynthesis, protein synthesis, dna/rna synthesis in condensation reactions

Endergonic

chemical reaction that absorbs energy

Exergonic

chemical reaction releases energy

catabolic reaction

the breakdown of larger molecules into smaller subunits (polymers into monomers)

how catabolic reactions work

chemical bonds are broken, so energy is released

e.g. cellular respiration, fermentation

biochemical pathway

an ordered series of different reactions, each controlled by enzymes, with the outputs of one reaction being the inputs for the next. the steps can occur in different cells or locations within a cell

why are biochemical pathways needed

• they are essential for cellular functions, transforming initial reactants through multiple steps to produce end products that cells need for energy, growth and repair

• e.g. photosynthesis, cellular repsiration

2 types of pathways

linear

cyclic: starting molecule needs to be regenerated at the end of the pathways so that cycle can continue

enzyme affinity

a measure of the ease with which an enzyme will bind to a substrate. it can be affected by chemical inhibition

enzyme inhibitors

substances that prevent the normal action of an enzyme, slowing the rate of reactions

irreversible inhibition

the inhibition permanently covalently binds to the enzyme. there is no reaction (cyanide)

reversible inhibition

the inhibitor is temporarily bound to to the enzyme via a non-covalent bond, preventing its function. reversible inhibitors are used to control enzyme activity

(heavy metals, leads, mercury)

competitive inhibition

an inhibitor molecule, structurally similar to the substrate, competes with the substrate binding to the same active site, preventing it from binding at normal rates

build up of end product may deactivate the enzyme in this way

non-competitive inhibitors

bind to the enzyme, but not at the active site, but alter its shape. the substrate may still be able to bind, but the reaction rate is slowed because the enzyme is less able to perform its function

allosteric enzyme inhibitors

a type of non-competitive inhibitor that induce a shape change that alters (but doesn’t block) the active site, preventing the substrate from binding. the enzyme ceases to function

feedback inhibition

the end product of a metabolic pathway inhibits an earlier enzyme in the pathway, reducing or stopping further production of that product.

does this by inhibitor and activator molecules binding with enzymes to change their state

enzyme concentration is regulated by

• controlling gene expression

• controlling the rate of degradation of the enzyme

• regulatory molecules and cofactors that bind to enzymes

• feedback inhibition

Effect of Temperature

• little activity at low temperatures, as molecules don’t have much kinetic energy and therefore dont collide often

• enzyme gradually increases as temperatures increases, as more energy increases the collision rate of enzyme and substrate molecules

• when optimum temperature is reached, rate of reaction is highest

• After this temperature, activity sharply decreases, as enzyme denaturation occurs

denaturation

the bonds maintaining the shape of the active site are disrupted and the enzyme can no longer bind to the substrate.

Effect of pH

• enzymes are affected by pH

• extremes of pH away from the enzyme optimum range can result in denaturation

• enzymes are found in very diverse pH conditions, so they must be suited to perform in these environments

Substrate concentration

• rate of reaction increases with increasing substrate concentration, as there are more substrate molecules per unit volume to react with the available enzyme, creating more enzyme-substrate complexes

• (differs from total quantity of substrate, which determines the max amount of product that can be made)

• the rate of plateaus when all active sites are full when all the enzyme active sites are saturated. a fixed amount of enzyme is assumed

substrate concentration and inhibition

• increasing substrate concentration can displace competitive inhibitors, because the molecules are still in motion

• non-competitive inhibitors are not displaced by increasing substrate concentration

enzyme concentration

(given a fixed amount of substrate…)

• the reaction rate increases with an increase in enzyme concentration until the substrate runs out.

• there are more agents per unit volume to bind with substrate, to catalyse the reaction, leading to more frequent enzyme-substrate interactions

• the same amount of product is made

• usually another factor becomes limited, leading to plateau

cofactor

enzymes need cofactors or helper molecules to function. they work by altering the shape of enzymes to make active sites functional or by completing the active site

cofactors can be

• inorganic such as minerals

• organic such as coenzymes or prosthetic groups

coenzymes

an organic molecule that acts as a cofactor. they carry/transfer electrons or ions from one reaction to another in a metabolic reaction

• they bind loosley

• temporarily modified during reactions but are regenerated and reused

prosthetic groups

• bind tightly and permanently

• e.g. heme in haemoglobin

ADP

adenosine di phosphate

a coenzyme classed as a nucleotide

• it is composed of adenine and ribose, making the adenosine part and two phosphate groups

• ADP combines with a 3rd phosphate group and an input of energy to become ATP, which provides usable energy for cells

where is atp from

• ATP is produced during cellular repiration where energy released from glucose forms the bond that connects ADP with a phosphate, in the process of phosphorylation

• atp synthase catalyses reaction

ATP

ATP is a portable energy carrier that moves around the cell to supply energy where required. It releases energy when it is hydrolysed to form ADP and Pi, breaking a phosphate bond, which releases energy.

cycling atp and adp

• atp can release its energy quickly by hydrolysis of the terminal phosphate

• this reaction is catalysed by ATPase

• once ATP has released its energy, it becomes ADP again (low energy)

• ADP is then phosphorylated again with more energy from glucose and the cycle continues

ATP synthase

an enzyme found that catalyses the formation of ATP from ADP and inorganic phosphate (Pi) using energy.

autotrophs

organisms that are capable of harnessing their own energy by making their own organic compounds

photosynthetic autotrophs

• plants, some unicellular protists, some bacteria

convert light energy of the sun into the chemical energy of organic molecules such as glucose

photosynthesis

transforms light energy of the sun into chemical energy of glucose

• carbon is fixed: incorporated into organic compounds using co2, h20 and sunlight

photosynthesis net reaction

6CO2 + 6H2O -light- C6H12O6 + 6O2

photosynthesis overall inputs and outputs

inputs: carbon dioxide, water, light

outputs: glucose, oxygen, water

chloroplasts

membrane bound organelles where photosynthesis takes place

• mainly in mesophyll cells between upper and lower epidermal layers

what are chloroplasts filled with

green light trapping pigment called chlorophyll which gives plants their green colour

wherer is chlorophyll located in bacteria

photosynthetic bacteria with no membrane-bound organelles, chlorophyll is located in the cytoplasm

chloroplast structure

• enclosed by a double membrane envelope

• third inner membrane system divides interior into compartments

  • thylakoid dics packed with chlorophyll

  • stacked into structures called grana

  • connected by thylakoid lamellae

• fluid stroma surrounds thylakoids

what does stroma contain

contains dna, dna and ribosomes used to synthesize some of the proteins within the chloroplast

pigment

a molecule that absorbs certain wavelengths of light and reflect all others

electromagnetic spectrum

light is a form of energy

visible light between 380nm and 750nm

photosynthetic pigments

absorb different wavelengths of light

two categories:

• chlorophylls

• carotenoids and xanthophylls are accessory pigments

category 1: chlorophylls

• the main photosynthetic pigments in plants

• absorb red and blue-violet light

  • chlorophyll a is the primary pigment. chlorophyll b is an accessory pigment that passes energy to chlorophyll a

category 2: carotenoids and xanthophylls

accessory pigments that appear orange, yellow or red

• they absorb light that chlorophyll can’t absorb (blue-green range)

• they pass some of the energy they harness to chlorophyll a

Light Dependent phase

The first stage of photosynthesis which occurs in the photosystems of the thylakoid membranes

Light Dependent phase Process

• light is trapped by chlorophyll in the thylakoid discs of grana

• sunlight excites an electron within the chlorophyll

• the light splits water in oxygen, H+ ions and electrons during photolysis

• oxygen is released as the first by-product out of the chloroplast

• NADP picks up electrons and H+ ions from water to become NADPH

• Excess H+ ions passes through ATP Synthase, providing the energy for the formation of ATP

Light Dependent phase inputs/outputs

Inputs: Light, Water, NADP, ADP + Pi

Outputs: Oxygen, NADPH, ATP

Light Independent Phase

the second stage of photosynthesis which occurs in the stroma of the chloroplast where carbon of co2 is fixed into organic compounds using H+ and the energy from ATP

Light Independent phase Process

carbon fixation occurs in the liquid stroma of chloroplast, catalysed by the enzyme rubisco

• in this step rubisco fixes CO2 to RuBP to make 3PG

• H+ ions from NADPH and energy from ATP are then added to make triose phosphate (simple sugar) used to form glucose and regenerate RuBP

• Two simple sugars join to make one glucose molecule, so 2 rounds of cycle make 1 glucose molecule

• NADP and ADP are unloaded and recycled to the LDP

careful to note with H+ ions in LIP

some of the H+ goes into producing water, using half of the O from CO2

Light Independent Phase Inputs/Outputs

Inputs: CO2, NADPH, ATP

Outputs: Glucose, Water, NADP, ADP + Pi

RuBisCo

a protein enzyme with one active site that can bind to two different substrates

substrates are a 5C intermediate compound and Co2

where is RuBisCo found?

in the stroma of chloroplasts

what does RuBisCo do?

It catalyses the first step of the Calvin Cycle bringing carbon into the cycle in a process called carbon fixation and fixes it into an 3C organic compound.

here is acts as a carboxylase

what RuBisCo does step by step

• in photosynthesis is captures co2 and adding it to RuBP, fixing carbon

• some of these are modified using NADPH and ATP to eventually create a glucose molecule

RuBisCo main feature

RuBisCo activity is one of the key elements limiting the rate of photosynthesis

loaded acceptor

a coenzyme that carries high-energy electrons after accepting them.(e.g. NADH, FADH₂)

unloaded acceptor

an oxidised coenzyme that can accept high-energy electrons (e.g. NAD⁺, FAD)

NAD,FAD,NADP

non protein nucleic acid coenzymes that bind with the active sites of enzyme to help them catalyse reactions. they shuttle electrons and protons between reaction in a cell

Photorespiration

Both CO2 and O2 can bind to Rubisco’s active site. However, at low temperatures (15-25) CO2 is more likely to bind.
As temperature increases, rubisco changes shape so more O2 binds and less CO2 binds. Instead of acting as a carboxylase, adding CO2 to RuBP it acts as an oxygenase adding O2 in a process called photorespiration

what does photorespiration produce

Produces a toxic product that wastes energy (ATP) and NADPH to metabolise and does not produce glucose, thus reducing the efficiency of photosynthesis. However, photorespiration rate is low at low to mild temperatures.

Main idea of C4 and CAM plants

• evolved to allow certain plants to minimise the wasteful process of photorespiration, by ensuring that rubisco always encounters high concentrations of CO2

• adapted to maximise the efficiency of photosynthesis at high temperatures

• both processes require more energy, so these plants grow slowly

what conditions are C4 and CAM plants adapted to

C4 plants are adapted to tropical conditions and the CAM plants are adapted to desert conditions

C4 plants general knowledge

• first organic compound made from carbon fixation is oxaloacetate (4C molecule)

• sugar cane, native grasses, corn, sorghum

C4 advantages

• capable of high rates of photosynthesis in hot humid environments and use water more efficiently

• higher yield of photosynthetic products compared to C3 plants, giving them an advantage in tropical enviros

• due to unique structural and psychological characteristics concentrate CO2 in cells around rubisco

• limits the exposure of rubisco to O2 preventing photorespiration

• optimum temp 25-40

C4 purpose

minimise photorespiration by separating the initial carbon fixation and the Calvin cycle in space

• LDP and initial carbon fixation occur in spony mesophyll cells. chloroplasts in these cells have no rubisco

• Calvin Cycle occurs in bundle sheath cells, which have chloroplasts w Rubisco, but low O2 (as no LDP here)

they increase photosynthetic rates by separating rubisco from O2 and delivering CO2 straight to the enzyme

C4 internal structure

• have more tightly packed mesophyll cells, that are tightly arranged around bundle sheath cells

• reduces intercellular air spaces, preventing accumulation of O2

• restricts diffusion of O2 from air spaces into bundle sheath cells

C4 process

• atmospheric CO2 is fixed in mesophyll cells to the 4C intermediate oxaloacetate by the enzyme PEP Carboxylase

• Oxaloacetate then converted to another C4 intermediate molecule malate, which is transported to the bundle sheath cells using ATP

• Inside bundle sheath cells, malate is broken down to release CO2 for rubisco to fix in the calvin cycle like c3 plants, to eventually produce glucose (even if hot, little O2)

photorespiration avoided, increasing rate of photosynthesis

PEP Carboxylase

has a high affinity for CO2 and does not binds to O2

CAM Plants Purpose

minimise photorespiration by separating carbon fixation and the calvin cycle in time

CAM Plants feaures

• dominate in Hot, Dry areas like deserts

• On hot/dry days stomata close to reduce water loss via transpiration (CO2 cant enter and O2 produced by photosynthesis builds up in air spaces)

• CAM plants open stomata at night when conditions are cooler, and harvest and store CO2

• CO2 is release during the day for the calvin cycle

• optimum temp >40

CAM process

• Carbon from CO2 is fixed into 4C oxaloacetate by PEP Carboxylase at night, and then converted into malate, which is stored in the large vacuoles of mesophyll cells

• during day CAM plants do not open stoma to prevent water loss

• malate is transported out of vacuole and is then broken down into CO2 during the day for use in the calvin cycle (still in mesophyll cells), to eventually produce glucose

• this controlled release maintains a high concentration of CO2 around rubisco, limiting its exposure to O2, and leading to very low rates of photorespiration

What is a factor that affects the rate of photosynthesis called

limiting factor

Factors affecting rate of photosynthesis

light intensity/availability/colour

water availability

Temperature

Carbon dioxide concentration

light intensity

• light is the energy source that drives photosynthesis

• low light intensity, rate of photosynthesis is low

• rate of photosynthesis increases within increasing light intensity, as there is more energy available to drive the process

• Until maximum rate is achieved, as indicated by a plateau (enzymes active sites in chloroplasts operating at full capacity = saturated)

• from this point increasing light intensity has no further effect on rate of photosynthesis

• as other factors become limiting

• (light is limiting factor up until plateau)

CO2 concentration

• CO2 is a reactant

• photosynthetic rate increases as CO2 concentration increases as there are more substrate molecules to bind with rubisco, until a max rate is reached

• rate of reaction plateaus when enzymes active sites are saturated

• at high concentrations, rate of photosynthesis slows as other factors become limiting, and impact concentration of the enzymes

Amount of Water

H2O is a reactant

• b/c amount of water used in photosynthesis is small compared to amount needed to keep cells alive, plant normally has sufficient water for photosynthesis to occur in nature

• does have an indirect effect on rate of photosynthesis

• when plant under water stress, stomata close, reducing gas exchange, therefore limiting the availability of CO2

• if more water present, stomata doesn’t close as often?

Temperature - photosynthesis

• reactions controlled by enzymes, which only function efficiently at optimal temp ranges

• lower temps: molecule collision rate is low, so reaction rate is low

• higher temps: enzymes become denatures, changes their shape, preventing them from catalyzing reactions

pH - photosynthesis

• enzymes function best at optimum pH

• as enzymes (like rubisco) control reactions of photosynthesis, process occurs at its highest rate at optimum pH values

• at pH values both above and below optimum, enzymes will denature, which will reduce rate of photosynthesis

enzyme concentration - photosynthesis

• rate of reaction increases w increase in enzyme conc. until substrate is consumed

• same amount of product made, just made more quickly

• reaction controlled by rubisco main limiting factor

• coenzyme concentration is limiting

glucose

the source of energy for cellular function, but cells can’t use the energy directly in glucose, they need to obtain energy from ATP

cellular respiration

the biochemical pathway by which organisms break down glucose, releasing energy for the synthesis of ATP.

energy not stored in chemical bonds is

lost as heat

Glycolysis location

occurs in the cytosol of the cell, does not require oxygen

Glycolysis process

• glucose is broken down into 2 pyruvate and a net 2ATP

• (4ATP produced in this process but 2 ATP are used)

• NAD+ is loaded with H+ and electrons to form NADH

Glycolysis aim

breaks down glucose into 2 pyruvate molecules and release a little energy