enzymes

enzymes: globular proteins that catalyse metabolic reactions

 anabolic: larger from smaller
 catabolic: smaller from larger
 required in small amounts
catalyst: molecule that speeds up chemical reaction, but remains unchanged at the end of reaction
for a reaction to occur, there must be an effective collision
activation energy
 as molecules react, they become unstable, high energy intermediates  energy needed to raise molecules to
transition state
 enzymes work by lowering activation energy
active site: depressions on enzyme surface, that fit shape of specific substrate molecules
specific in action due to unique 3D shape at active site

steps of enzymatic reaction

1. shape of active site of enzyme is specific and complementary to shape of substrate
upon effective collisions between E and S, E-S complex is formed
2. interactions between E and S molecules strain chemical bonds within substrates  lowers activation energy
3. when reaction finished, products no longer fit into active site, released. enzymes are released

lock and key hypothesis
as E-S complex formed, the substrate is raised in energy to
a transition state, then broken down into products +
unchanged enzyme
exact fit between substrate and enzymes
induced fit hypothesis (accounts for simultaneous
binding and chemical change observed in most reactions)
at active site, arrangement of certain amino acids in
enzyme exactly matches certain groupings on substrate,
forming E-S complex
and essential, critical change of shape caused in enzyme
 momentarily raised substrate to transition state

effect of temperature on rate of reaction

1. describe: when temperature increases from X to Y, rate of reaction increases from A to B
explain:
 enzymes inactive at low temperatures due to low KE  frequency of effective collisions is low
 as temp increases, KE of substrate and enzyme increase  frequency of effective collisions increase
 increase rate of formation of ES complex  increase rate of reaction
2. describe: enzyme activity highest at B at its optimum temperature of Y
explain:
 all enzyme active sites occupied
3. describe: when temperature increased beyond Y to Z, rate of reaction decreases from B to C
explain:
 high temperatures break bonds that keep protein in specific shape
 active site loses original shape, no longer complementary to substrate
 denatured, loses catalytic function
 rate of denaturation increases at higher temperature

basically: KE  effective collisions, form ES complex

optimum all occupied
high temperatures break bonds, shape, denatured, rate

effect of pH on rate of reaction

1. describe: QD of optimum pH
explain:
 all enzymes have an optimum pH, work most efficiently  rate of reaction is maximum
 enzyme maintains specific 3D conformation  enzyme active site complementary to substrate
 enzyme binds to substrates to form ES complex  substrate converted to products
2. describe: changes in pH (specific) affect enzyme activity (QD)
explain:
 structure of protein maintained by various bonds
 changes in pH alter bonding pattern  3D shape of active site
 substrate no longer complementary to active site
 no ES complex  no product
 denatured, loses catalytic function
transport in plants
xylem: water & mineral salts
phloem: manufactured foods
collectively, they are known as vascular bundles

* xylem inside, phloem outside

therefore xylem on top
xylem bigger in roots

xylem tissue
structure function
long hollow tubes without end walls no obstruction to water flow  continuous movement of water by mass flow
hardened by lignin able to resist negative pressure without collapsing in on itself + structural
support for plant
impermeable to water able to transport water and dissolved mineral salts from roots to all other parts
pits in walls lateral movement of water to surrounding tissue

phloem tissue
sieve tubes and companion cells
 sieve tubes: narrow elongated elements connected end to end
 cytoplasm contains no nucleus of many other organelles
 each sieve tube connected to a companion cell  services and maintains cytoplasm of sieve tube
translocation: manufactured food moved around in the plant, through phloem tissue of vascular bundles
living tissue: high rate of aerobic respiration during transport (requires energy)

xylem phloem
one-way two-way
water and mineral salts food
no end walls between cells cells have end walls with perforations

root hairs
cells of root cortex have lower WP than soil  water moves into root hair cell by osmosis
active uptake/diffusion of soluble ions into roots (depends on concentration in soil compared to root hair cells)

movement of water has 2 main forces

1. root pressure
a. active transport of ions into root xylem vessels lowers WP
b. water flows in by osmosis  accumulates  flows up a few metres
2. transpiration
transpiration
process through which water vapour is lost from aerial parts of plants
 evaporation of water at surface of mesophyll cells into air spaces (mesophyll cells have thin film of moisture)
 diffusion of water vapour out stomata, down water vapour concentration gradient
stomata: pores in epidermis, each surrounded by 2 guard cells

transpiration stream: flow of water up stem

2 special properties of water
 cohesion: individual water molecules stick together because of hydrogen bonding
 adhesion: individual water molecules cling to surrounding surfaces  adheres to most surfaces, drawn up in long
columns without breaking
explanation
 as water leaves xylem vessels in leaf, tension is set up on the entire water column in xylem
 does not break or pull away from side of xylem vessels  cohesive and adhesive properties
 flow of water up the plant in transpiration stream
 water moves up xylem without any energy expenditure by plant

how do plants control transpiration?

a plant must make a trade-off between need for CO2 and water
stomata open and close to adjust transpiration rate to changing environmental conditions
guard cells change shape

when guard cells take up water, stomata open

 potassium actively taken up by guard cells
 lowers WP, so water enters by osmosis
 uneven cell walls cause guard cells to bow
 bowing causes pore of stomata to open

stomata close when water leaves guard cells

 diffusion of K+ ions out
 increases WP, water leaves by osmosis
 flaccid, stoma closes

factors that influence transpiration

1. humidity: lower, increase
a. increase water vapour concentration gradient between leaf and atmosphere
b. increase water evaporation
2. temperature: higher, increase
a. increases heat energy  increase water evaporation
3. wind: high
a. stronger wind blows away saturated away from around leaves
b. maintaining water vapour concentration gradient between leaf and atmosphere
4. light intensity: high
a. sunlight stomata open and wider
5. water supply
a. leaf cells turgid, stomata remains open

role of transpiration
 evaporation has strong cooling effect
 passively carry dissolved ions in transpiration stream
 all cells will receive water
 turgor pressure: support for plant

wilting (transpiration > absorption)

 cells flaccid
 reduce surface area of exposure to sunlight
 flaccid guard cells close stomata
 reduce transpiration
o photosynthesis is reduced as less water, CO2 and leaf area for sunlight
photosynthesis
structure function
petiole (leaf stalk) holds leaf, absorb more light
thin broad lamina larger SA for max absorption
thin for short diffusion distance
thin so light reaches all mesophyll cells
waxy cuticle reduce water loss through evaporation
(transparent for light to enter)
stomata open in presence of sunlight for exchange of CO2 and O2
chloroplasts (in mesophyll cells) absorbs and transforms light energy
more chloroplasts in upper palisade more light near leaf surface
air spaces in spongy mesophyll rapid diffusion of CO2 and O2
xylem and phloem close to mesophyll cells xylem water & mineral salts, phloem sugars away from leaf

chloroplasts
found in mesophyll and guard cells
double membrane organelle where all reactions of photosynthesis occur
inner membrane folds inwards  thylakoid membranes (branching membranes)  suspended in stroma

structure function
double contains grana and stroma
membrane permeable to O2, CO2, ATP, sugars
chlorophyll large SA, max absorption
pigments on
thylakoid
membranes
thylakoid restricted regions  accumulation of
spaces in grana protons, establishment of gradient
stroma enzymes for light-independent reactions

photosynthesis overview
use sunlight energy to produce organic molecules (sugars) from inorganic raw materials CO2 and H2O
oxygen is the by-product

redox reaction
oxidation: gain oxygen, lose electrons/H
reduction: lose oxygen, gain electrons/H
* H2O oxidised to O2
* CO2 reduced to sugar

chlorophyll: important light-absorbing pigment

what happens?
 2 interconnected stages complex set of reactions in chloroplast
 light energy absorbed by chloroplast pigments (light dependent)  drives reaction of light independent stage,
produces complex organic compounds

light dependent stage (grana)

photochemical step  unaffected by temperature
 photolysis splitting of water by light energy
 formation of reduced NADP (accepts hydrogen to form NADPH)
 energy transfer to ATP (ADP and phosphate)
 oxygen as by-product  rate of O2 produced indicates rate of photosynthesis
light independent stage (stroma)
catalysed by enzymes (temperature sensitive, light activated)
dependent upon supply of NADP and ATP
CO2 fixed to form 3C sugars

start from carbon dioxide

1. carbon fixation
 CO2 diffuses into stroma
 combines with ribulose biphosphate in the presence of rubisco (CO2 fixation enzyme)
 forms 2x glycerate-3-phosphate
2. reduction
 using energy from oxidation of NADPH and energy from ATP (light-dependent)
 2x glycerate-3-phosphate is reduced to 2x triose phosphate
3. regeneration of RuBP
 for every 6 molecules of TP
 5 goes to making 3 RuBP (regenerated, using energy from ATP)  so more CO2 can be fixed
 1 goes to product synthesis: lipids, amino acids and carbohydrates

limiting factors of photosynthesis

at any time, rate of photosynthesis is limited by factor in shorter supply
 light intensity
 CO2 concentration
 temperature
compensation point: no net loss/gain in CO2 (all from respiration taken in for photosynthesis)

temperature: enzyme graph shape

“since XXX is the limiting factor”, YYY has little effect on rate of photosynthesis”
just logic it out
respiration
living things need a continuous transfer of energy to break down nutrients
green plants: autotrophic, but animals are heterotrophs
need for energy anabolic reactions, active transport, movement, cell division

adenosine triphosphate
 relatively small and soluble
 phosphorylated molecule with 3 phosphate groups
when hydrolysed, it loses a phosphate group and energy is
transferred (ATP  ADP + Pi)
each cell makes its own ATP by respiration

important features of ATP

 moves easily within cells and organisms by facilitated
diffusion
 the hydrolysis of one ATP releases a small amount of
energy  just the right size to fuel a particular step in
process
o glucose contains far too much  wasteful use

other nucleotides to know

 coenzyme: molecule required for enzyme to be able to
catalyse a reaction
 NAD and FAD: hydrogen acceptors  without these,
dehydrogenase enzymes cannot remove hydrogen from
substrates
 CoA: involved in removal of carbon fragments

mitochondria structure
 cytosol  glycolysis
 matrix of mitochondrion  link reaction + Krebs cycle
 inner membrane of mitochondrion  oxidative phosphorylation
o SA increased by intucking to form cristae
o impermeable to H+  potential difference between intermembrane space and matrix
 intermembrane space  accumulation of H+

overview tables
stage ATP NADH FADH2
1 2 2
2 2
3 2 6 2
4 28

glycolysis (cytosol)
 glucose  pyruvate
 2 molecules of ATP to activate glucose, 4 molecules of ATP out  net gain of 2 ATP
 pyruvate is a 3-carbon sugar
outputs: ATP, NADH

link reaction
 links glycolysis with Krebs cycle
 pyruvate diffuses from cytosol to matrix
 oxidative decarboxylation
o oxidative: remove H, given to NAD  2NADH
o decarboxylation: remove CO2
 get acetyl  combines with coenzyme A to form acetyl CoA
krebs cycle
acetyl CoA (2C) + oxaloacetate (4C)  citrate (6C) + CoA (reused)
Krebs cycle turns twice for each molecule of glucose
input: 2 acetyl coA, 2 ATP, 6 NAD, 2 FAD
output: 2 ATP, 6 NADH, 2 FADH2, 2 CO2

electron transport chain and oxidative phosphorylation (inner membrane and intermembrane space of mitochondria)
 NADH and FADH2  lose hydrogens, which split into H+ and e-
o NADH x 2.5 = ATP
o FADH x 1.5 = ATP
 electrons transported along series of carries (electron transport chain) (inner membrane of mitochondria)
 oxygen is the final electron acceptor  produces water with protons
 inner membrane of mitochondria  barrier to ions and electrons
 H+ pumped by carrier proteins, using energy of oxidation  intermembrane space
 gradient in H+ concentration  build up potential difference and potential energy
 H+ flows back into matrix, through ATP synthase, down concentration gradient
 generated energy energy transferred to synthesis of ATP from ADP + Pi  chemiosmosis
output: 28 ATP

anaerobic respiration
net gain: 2 ATP from glycolysis

alcoholic fermentation: glucose  ethanol + carbon dioxide + energy (yeast and plants)
2 pyruvate  2 CO2 removed  2 ethanal  alcohol dehydrogenase, 2NADH becomes 2NAD  2 ethanol

lactic acid fermentation: glucose  lactic acid + energy (vertebrate)

2 pyruvate  lactate dehydrogenase, 2NADH becomes 2NAD  2 lactic acid

limited yield from anaerobic respiration (substrate level phosphorylation) compared to aerobic respiration (oxidative
phosphorylation)
wasteful of respiratory substrate (ethanol and lactate contain unused chemical energy)
lactic acid fermentation  O2 debt
 after prolonged strenuous exercise, lactate builds up in muscles
 carried in blood stream to liver to be converted back to glucose
 requires energy from respiration  oxygen debt (extra)
breathing and smoking

respiratory system
need for respiratory system: SA:V decreases with larger organism, water tight/skin not suitable for gaseous exchange
1. ventilation mechanism (breathing in lungs)  maintain concentration gradient for diffusion
2. circulation system (circulatory system)  maintain concentration gradient for diffusion
3. haem protein (haemoglobin)  combine with oxygen, increase gas carrying ability
pharynx  larynx  trachea (connect lung with pharynx)  bronchi (1 for each lung)  bronchioles  alveoli
diaphragm: sheet of muscle
pleural cavity: contains pleural fluid (lubricating)
thorax: dome shaped chamber formed by rib cage, intercostal muscles and diaphragm

to protect delicate lining of alveoli air must be warm, moist and free of dust/foreign particles
 nostrils: hairs trap large dust particles, blood vessels warm air slightly
 trachea and bronchi: lined with ciliated epithelium & goblet cells
o sticky mucus moistens incoming air, traps finer dust
o ciliated epithelium beats mucus into buccal cavity swallowed
smooth muscle and cartilage prevents collapse of air tubes, regulate size of smaller airways
 at each division: amount of muscle increases, cartilage decreases

breathing: inhalation and exhalation

 thorax is air-tight  change in volume will cause change in pressure
1. inhalation
a. external intercostal muscles contract, ribs up and out, diaphragm down
b. increase volume of thorax, decrease pressure
c. pressure reduced below atmospheric pressure  air is drawn in
2. exhalation
a. external intercostal muscles relax, ribs down and in. diaphragm up
b. decrease volume of thorax, increase pressure
c. pressure above atmospheric pressure  air flows out

gaseous exchange
alveoli (and terminal bronchioles)  elastic connective tissue, expands/recoils with inhalation/expiration
capillary systems wrap around clusters of alveoli
wall of alveolus is one cell thick
capillaries very narrow, just 1 RBC at a time
how to maintain concentration gradient?  continuous flow of blood + movement of air in and out

oxygen carbon dioxide

1. one cell thick alveolar wall is permeable to O2 1. tissue cells produce a lot of CO2 during respiration
2. concentration of O2 is higher in alveolar air, 2. diffuses into blood, enters RBC
compared to blood 3. dissolves in water to form carbonic acid (catalysed
3. O2 dissolves in thin film of moisture, diffuses by carbonic anhydrase)
into blood capillaries 4. carbonic acid becomes hydrogen carbonate ions,
4. O2 combines with haemoglobin in RBCs, forms which diffuse out of RBCs, carried in blood plasma
oxyhaemoglobin 5. HCO3- ions diffuse back into RBCs in lungs,
5. when blood passes through low oxygen converted to carbonic acid then CO2 and H2O
tissues, oxyhaemoglobin releases oxygen, 6. diffuses into alveoli, exhaled
diffuse into cells

smoking
affects respiratory and cardiovascular system
chemicals properties effects
tar carcinogenic increases risk of lung cancer
nicotine stimulating, relaxing, releases dopamine addictive
increase heart rate and blood pressure increased risk of blood clots due to decreased blood flow
carbon combines irreversibly with haemoglobin blood able to transport less oxygen
monoxide to form carboxyhaemoglobin
irritants paralyses cilia lining air passages dust particles in mucus cannot be moved
chronic obstructive pulmonary disease
 cigarette smoke stimulates secretion of mucus + inhibits cilia movement
 mucus accumulates in bronchioles (contains carcinogenic compounds)
 alveoli loses elasticity

COPD(1) – chronic bronchitis

 long term cough and phlegm
 bionchi inflamed
 casues goblet cells to produce excess mucus + cilia beat less strongly
 mucus with dust accumulates, have to be coughed up forcefully  persistent cough
 tissues in airways damaged, stiffer
 bronchioles narrow breathing difficult

COPD(2) – emphysema
 alveoli walls lose elasticity, destroys lung tissues  cannot exhale properly
 inflammation of lungs: macrophages release hydrolytic enzymes  break down elastic fibres
 alveoli left over-inflated, air trapped
 small holes in walls  reduce SA for gaseous exchange
 permanent breathlessness

lung cancer
 persistent exposure of bronchi to tar/carcinogens
 damage to goblet cells
 may trigger permanent DNA mutations
 smoking increases risk of all cancers
 symptoms: pain in rib, coughing up blood