Biology

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What role do hydrogen atoms play during respiration

• The substrate molecules are broken down and the hydrogen atoms become available

• Hydrogen carrier molecules NAD and FAD take h turn into nadh/fadh2 and transfer to the inner mitochondrial membrane

• nadh/fadh2 release the hydrogen atoms which split into protons and electrons

• The protons are pumped across the inner mitochondrial membrane into the intermembrane space - forming a proton / chemiosmotic gradient

• This proton gradient is used in chemiosmosis to produce ATP

• After the protons have flowed back into the matrix of the mitochondria via ATP synthase they are oxidized to form water

Structure of mitochondria

• Mitochondria have two phospholipid membranes, an outer and an inner membrane

• The outer membrane

  • Smooth

  • Permeable to several small molecules

• The inner membrane

  • Folded (cristae)

  • Less permeable

  • The site of the electron transport chain (used in oxidative phosphorylation)

  • Location of ATP synthase (used in oxidative phosphorylation)

• The intermembrane space:

  • Has a low pH due to the high concentration of protons

  • The concentration gradient across the inner membrane is formed during oxidative phosphorylation and is essential for ATP synthesis

• The matrix:

  • Is an aqueous solution within the inner membranes of the mitochondrion

  • Contains ribosomes, enzymes and circular mitochondrial DNA necessary for mitochondria to function

Structure and function of mitochondria

Cristae
- Large surface area holding many electron transport chain proteins & atp synthase = more atp.

4 stages of aerobic respiration.

1. Glycolysis	Phosphorylation and splitting of glucose	Cell cytoplasm
2. Link reaction	Decarboxylation and dehydrogenation of pyruvate	Mitochondrial matrix
3. Krebs cycle	Cyclical pathway with enzyme-controlled reactions	Mitochondrial matrix
4. Oxidative phosphorylation	Production of ATP through oxidation of hydrogen atoms	The inner membrane of mitochondria

Aerobic respiration definition

process of breaking down a respiratory substrate in order to produce ATP using oxygen

Coenzyme

helps an enzyme carry out its function but is not used in the reaction itself

Krebs cycle

• The Krebs cycle (sometimes called the citric acid cycle) series of enzyme-controlled reactions

• Acetyl CoA (2C) enters the circular pathway via the link reaction

• 4 carbon (4C) oxaloacetate accepts the 2C acetyl fragment from acetyl CoA to form citrate (6C)

• Citrate is then converted back to oxaloacetate through a series of small reactions

Series of small reactions for citrate to oxaloacetate

1. 4c oxaloacetate reacts with acetyl CoA, oxaloacetate gets 2 carbons from it = 6C citrate, CoA released for link reaction.
   2. decarboxylation and dehydrogenation, nad → nadh = 5C
   3. decarboxylation and dehydrogenation, nad → nadh 4C

4. Atp produced = adp + Pi

5. 2 more dehydrogenation reactions, fad THEN nad

6. oxaloacetate formed again

happens twice for each glucose molecule

Role of nad and fad

• Reduced NAD and reduced FAD transfer the hydrogen atoms (hydrogen ions and electrons) from the different stages of respiration to the electron transport chain on the inner mitochondrial membrane

  • This is the site where hydrogens are removed from the coenzymes)

  • Electrons from reduced NAD (NADH) and reduced FAD (FADH₂) are given to the electron transport chain

  • Hydrogen ions from (NADH) and (FADH₂) are released when the electrons are lost

  • The e transport chain moves these (protons) across the inner mitochondrial membrane into the intermembrane space, creating a proton gradient (more protons in the intermembrane space)

  • The movement of protons down the proton gradient, back into the mitochondrial matrix, gives the energy required for ATP synthesis

How much nad and fad in those reactions gng

krebs = 6 nadh 2 fadh2

glycolysis = 2 nadh

Link = 2 nadh

oxidative phosphorylation

• h atoms donated by nadh/fadh2, split into h+ and e

• e release Energy as move through e transport chain

• released Energy used to transport h+ across inner mitochondrial, from matrix to intermembrane.

• conc gradient of h+ made

• h+ return to matrix via facilitated diffusion through channel protein atp synthase

• diffusion provides E for atp synthesis, adp+pi→atp+h20

• o2 combines with h+ & e- to form water at end of transport chain

Consequences of no o2 in respiration

• There is no final acceptor of electrons from the electron transport chain

• The electron transport chain stops functioning

• No more ATP is produced via oxidative phosphorylation

• Reduced NAD and FAD aren’t oxidised by an electron carrier

• No oxidised NAD and FAD are available for dehydrogenation in the Krebs cycle

• The Krebs cycle stops

what type of anaerobic resp do certain organisms use

• Yeast and microorganisms use ethanol fermentation

• Other microorganisms and mammalian muscle cells use lactate fermentation

Ethanol fermentation

• glycolysis takes place as usual (net gain 2 atp) (4 atp gained - 2atp used for glucose)

• 2pyruvate gained

• 2pyruvate decarboxylated to 2ethanal (2ch3cho)

• 2ethanal→2ethanol, because nad gives hydrogens from glycolysis (nad regenerated)

• alcohol dehydrogenase used for ethanal to ethanol

lactate fermentation

• glycolysis takes place as usual (net gain 2 atp) (4 atp gained - 2atp used for glucose)

• 2pyruvate gained

• nad is regenerated by giving 4 hydrogens to 2pyruvate → 2lactate (pyruvate to lactate needs lactate dehydrogenase)

what happens to lactate after being formed

• taken to liver where either turned into pyruvate for link reaction

• or glycogen for energy storage

Chloroplast pigments

Pigment group	Name of pigment	Colour of pigment
Chlorophylls	Chlorophyll a	Light green
	Chlorophyll b	Dark green
Carotenoids	β carotene	Orange
	Xanthophyll	Yellow

Outline need for energy in organisms

• anabolic reactions

• Active transport

• movement

• bioluminescence

Examples of anabolic reactions

• Dna replication

• protein synthesis

• active transport

• movement

• phosphorylation

How is atp suitable as universal currency

• small

• water soluble

• easily transported around cell

• easily hydrolysed

• large quanitity of energy released

• rapid turnover rate

• readily available

atp equation

atp + h20 →←adp + pi

chemiosmosis

occurs in mitochondria inner membrane & thylakoid membrane

• e transport chain makes h+ conc gradient

• high energy e move from carrier to carrier, Energy released used to pump h+ across inner membrane to intermembrane space, matrix to intermembrane space

• protons move down gradient releasing Energy

• h+ move through atp synthase complex, uses released E to phosphorylate adp.

• o2 accepts h+ & e- formng h20

• makes most of atp, 32/34 atp per glucose.

atp structure

adenine ribose and 3 phosphates

2 ways atp synthesised

substrate level phosphorylation

• uses energy from another chem reaction for adp+pi

chemiosmosis

glycolysis

link reaction

Absorption spectra

An absorption spectrum is a graph that shows the absorbance of different wavelengths of light by a particular pigment

action spectra

An action spectrum is a graph that shows the rate of photosynthesis at different wavelengths of light

Pigments and what they absorb

Pigment group	Name of pigment	Colour of pigment
Chlorophylls	Chlorophyll a	Light green
	Chlorophyll b	Dark green
Carotenoids	β carotene	Orange
	Xanthophyll	Yellow

Rf values of pigments

• Carotenoids have the highest R_f values (usually close to 1)

• Chlorophyll B has a much lower R_f value

• Chlorophyll A has an R_f value somewhere between those of carotenoids and chlorophyll B

Purpose of photosynthesis

Produce organic molecules

sites of light dependent reaction

granum/thylakoid

sites of light independent reaction

stroma

Why do photosystems have different pigments

To increase the range of absorbed wavelengths of light

Function of photosystem

pigments absorb different wavelengths of light.
Transfer energy to reaction center, causing photoactivation of reaction center.
High energy electron released from reaction centre

PSI vs PSII

PSII has a oxygen evolving complex enzyme

Purpose of light dependent reaction

Use light energy to get ATP & Reduced nadp for light independent reaction

non cyclic phosphorylation

light hits PSI, electrons are excited out to the enzyme, produces reduced NADP.

light hits PSII, photoactivation, electrons moves through etc to PSI.

Protons pumped into thylakoid from energy from electron. Proton gradient formed.

Protons move out through atp synthase, produces atp.
electron in PSII replaced from e- from photolysis of h20 catalyzed by oxygen evolving enzyme complex. O2 waste product.

Cyclic photophosphorylation

Light absorbed by pigment in PSI, causing photoactivation of reaction center, releasing high energy e-.

Goes through etc, then returns to PSI.
This powers etc, pumps protons into thylakoid, protons leave via facilitated diffusion via atp synthase.

Produces atp.

Differences & similarities between cyclic and non-cyclic photophosphorylation

similarities:

happens in thylakoid/granum

uses PSI

produces atp

differences: (happen in non cyclic)

Uses PSII
Produces NADPH

Photolysis of h20

Calvin cycle/light independent reaction

start with rubp (5C)

1. Carboxylated, catalysed from rubisco

2. Forms 6C unstable molecule, splits apart into 3C glycerate 3-phosphate.

3. Hydrogenated by NADPH, uses 1 atp.

4. Forms TP, uses 1 atp to turn back into rubp. (5/6 TP used for this)

Uses of TP & GP

TP:

• Hexose sugars

• starch (energy storage)

• sucrose (translocation in phloem)

• cellulose (cell wall)

• amino acids (when ammonium/nitrate is added)

GP:

• fatty acids & glycerol

• phospholipids & triglycerides

Limiting factors in photosynthesis

temp

co2 conc

strength of light

How do factors affect the systems in photosynthesis

• more light

• more absorption by pigment

• high rate of light dependant reaction

• more atp and nadph for calvin cycle

More co2

• more rubp carboxylation

• high rate of light independant reaction

• more organic compounds produced

More temp

• optimum = more enzyme substrate complexes formed (rubisco, atp synthase, nadp reductase)

• higher rate of light independant reaction

Too much temp

• enzymes denature (H bonds break in between)

• very low rate of photosynthesis

Structure of chloroplast relate to function

• Stroma for light independant reaction

• Large number of grana to absorb more light

• Stroma colourless so light reaches thylakoids

• DNA for chloroplast protein production

• starch grains to store chemical energy

Homeostasis def

• maintaing an optimum internal environment

Examples of internal environments

• body temp

• h20 conc in blood

• glucose conc in blood

Negative feedback

• Body undergoes change from optimum condition (stimulus)

• stimulus detected by receptor

• signal sent to control centre

• control centre sends signal to effector

• effector produces response to correct the change

Excretion

• Removal of waste products in our body

Deamination

• removal of amine group (nh2) in liver

• Nh3 and keto acid produced

• keto acid used in respiration

• nh3 = soluble = toxic

• nh3 + co2 → urea = removed by kidney

Kidney function

• Carries out excretion

• helps wt homeostasis

Nephron

• Strucutre that produces urine made out of bowmans capsule and tubules

Nephron diagram

Ultrafiltration

• High pressure causing substances to separate from blood

• Filters out h2o salts urea glucose amino acids

• High pressure in glomerulus generated by difference in diameter of afferent and efferent arteriole. Lwk tight asl

• Gaps in glomerular wall prevent RBC from leaking out.

• Basement membrane filters out plasma/large proteins, mr>67000.

• Podocytes = inner bowmans capsule wall allow filtrate to leak through in controlled amounts.

Selective reabsorption

• Most water is reabsorbed as it moves through the nephron. Rest is turned to urine.

• PCT reabsorbs all glucose and amino acids, most h2o, and some salts and urea.

• Loop of henle reabsorbs some H2O and salts (tad bit urea)

• Collecting duct reabsorbs some water.

• Leftover stuff is urine.

PCT adaptations

• 1 cell thick wall of PCT

• Capillary right next to it

• Tight junction in between pct cells to prevent leakage of filtrates.

• PCT wall has microvilli facing PCT lumen, and basal membrane facing capillaries.

• Microvilli to increase surface area to contain more co-transporter proteins for more reabsorption.

• Basal membrane has Na+/K+ pumps. and transport proteins for glucose/amino acid.

• Many mitochondria in PCT cell to produce ATP for active transport.

Selective reabsorption in PCT

• PCT cells pump out Na+ into the blood by active transport
  

• creates a Na+ concentration gradient between the PCT cells and PCT lumen
  

• Na+ and glucose enters the cell through co-transport (Na+ and amino acids too)
  

• glucose and amino acids get reabsorbed from cells to blood through facilitated diffusion
  

• water is reabsorbed through osmosis
  

• some urea will be accidentally reabsorbed due to diffusion.

Osmoregulation

• Control of water potential of the blood and tissue fluid.

Selective reabsorption in collecting duct

• Posterior pituitary gland releases ADH when the amount of water in the blood is low
  

• ADH binds to the receptor on the Collecting Duct cells
  

• it activates phosphorylase enzyme within the Collecting Duct cells
  

• vesicles with aquaporin will fuse to the cell surface membrane
  

• this increases the permeability of the Collecting Duct to water
  

• more reabsorption of water occurs
  

• this decreases the volume of urine, making it more concentrated

How our cells process glucose

First, Glucose diffuses into the cells using GLUT proteins (Glucose Transport Proteins)

To ensure the glucose remains trapped in the cell, glucose is phosphorylated (added with phosphate) so they cannot escape. This is catalyzed by glucokinase.

Some of the glucose will then be broken down in respiration to produce ATP.

Excess glucose molecules are converted into glycogen, by an enzyme; glycogen synthase.

Action of insulin

• Blood glucose concentration higher than normal.

• Detected by receptors in islets of Langerhans.

• B-cells secrete more insulin.

• Insulin stimulates skeletal muscle cell to cause vesicles with GLUT to fuse with cell surface membrane, cell glucose permeability increased. (only for skeletal muscle cells)

• Glucose diffuses into liver cells through GLUT proteins.

• Insulin activates glucokinase enzyme to phosphorylate glucose to prevent its escape bc glut proteins cant transport phosphorylated glucose.

• Insulin increase respiration of glucose.

• Insulin activates glycogen synthase, converts excess glucose into glycogen.

Action of glucagon

• Blood glucose concentration lower than normal.

• Detected by islets of Langerhans in pancreas.

• Alpha cells secrete more glucagon.

• Only affects liver cells.

Endocrine vs nervous

Hormones vs electrical impulse
Slow vs faster
Low atp vs high atp

Sensory neurone function

• transmit impulses from receptor to relay neurone

Relay neurone function and location

• transmit impulses from sensory to motor neurones.

• Only in CNS

motor neurone function

• transmit impulses from relay neurone to effector

Dendrites

• Increase surface area when receiving signals

• receive incoming signals (neurotransmitters) from other neurons at the synapse and transmit these electrical impulses toward the cell body

Sensory vs motor neurone

similarities

• Cell body wt nucleus

• Axons (elongated structures to transmit impulses over long distances)

• Dendrites (branched structure to increase surface area for receiving signals)

• Terminal branches with synaptic knobs

• Axons may have myelin sheath

Differences
- Cell body of motor neurone in CNS.

• Function (sensory is receptor to CNS etc)

Action potential def

• rapid change in the electrical charge distribution across a cell surface membrane.

resting membrane potential

• Before the neurone can send an impulse, it first has to generate and maintain a resting membrane potential of -70mV.
  

• This uses the Na+/K+ pump, that actively pumps out 3Na+ and pumps in 2K+ into the axon.

Depolarisation

• Resting membrane potential created first

• Voltage gated Na+ channels open

• Na+ rush into axon down conc gradient.

• Inside has higher voltage than outside, at +30mv voltage gated Na+ channels close.

Repolarisation

• At +30mv voltage gated Na+ channel close, but K+ voltage gated channel opens.

• K+ Rushes out down concentration gradient.

• Goes slight beyond resting potential and voltage gated K+ channel closes to -80mv.

refractory period

• period of time where axon is unresponsive to stimulus

how does action potential move along axon

• Strong stimulus

• 1 section of axon depolarises

• Local circuits cause next section of axon to depolarise.

Myelin sheath function

• provides area of insulation so ions cannot pass through

• Nodes of ranvier no electrical insulation, ions can pass through

• Speeds up action potential

Synapse

• Junction between 2 neurones

Cholinergic synapse

• Impulse reaches end of presynaptic neurone.

• Voltage gated Ca2+ channels open causing Ca2+ ions to rush in

• Vesicles move towards cell surface membrane.

• exocytosis of ACh (acetylcholine)

• ACh diffuses across synaptic cleft.

• ACh binds to complementary receptors on postsynaptic neurone.

• Ligand gated Na+ channels open, Na+ rush in.

• Postsynaptic membrane depolarises and a new action potential is generated.

• ACh detaches from receptor and is broken down by acetylcholinesterase.

• Into acetate and choline.

• Choline reabsorbed by presynaptic neurone and regenerated back into ACh.

Role of synapse

• Ensure impulses travels in one direction.

• Presynaptic contains vesicles wt neurotransmitters, post synaptic contains receptors.

• Allow interconnection of nerve pathways

• Individual neurones can connect with multiple other neurones = more efficient response.

How do receptor generate action potential

• Na+ causes Na+ channels to open

• Na+ rush in

• Receptor cells depolarise.

• Ca2+ channels open and Ca2+ rush in.

• exocytosis of neurotransmitters.

• depolarisation in sensory neurone.

Myofibril

• Dark and light parts

• Thick and thin filaments.

• dark = myosin light = actin

• Myosin has M line, actin has Z line

• Distance between Z lines = sarcomere.

Filament structure

Actin Filaments are THIN filaments:
made out of actin globular proteins, Troponin and Tropomyosin (prevents actin & mysin heads from attaching)

• Myosin Filaments are THICK filaments:

• made out of Myosin heads that face away from the M-line

• myosin heads can also function as an ATP-ase enzyme; to hydrolyse ATP into ADP + Pi

Zones in myofibril

Sliding filament theory

• Myosin head pulls actin filaments closer together (cross links) making the sarcomere distance shorter.

• Ca2+ binds to troponin on actin filament

• Causes tropomyosin shape to change, exposes actin filaments to myosin head.

• Myosin head attaches to the actin filament.

• Myosin head tilts back towards M-line, pulling actin filament in process.

• Sarcomere distance reduces.

• Myosin head hydrolyses ATP into ADP + Pi, releasing the molecules.

• Myosin head detaches from actin filament.

• New atp molec reattaches to myosin head and restarts whole process.

Neuromuscular junction

1. Depolarization/Action potential along motor neurone axon
2. Ca2+ channel opens and Ca2+ rushes in
3. Vesicles with ACh moves to the cell surface membrane
4. Exocytosis of ACh and diffusion of ACh along the neuromuscular junction
5. ACh binds to receptors on the sarcolemma
6. Na+ channel opens and Na+ rushes into the skeletal muscle fibre
7. Depolarization of sarcolemma, which causes depolarization of T-Tubule
8. Ca2+ transporters pump out Ca2+ into the sarcoplasm which binds to troponin on the Actin Filament

Why do venus flytraps eat insects

• Grow in places where there is not enough nitrogen in soil.

• Insects provide nitrogen that plants need for nucleotides or amino acids.

Venus fly trap structure

Venus flytrap whole process

• Insect stimulates sensory hairs twice withing 20-35 seconds.

• Ca2+ channels open and Ca2+ rush in generating action potential.

• Travels along cells

• Leaf lobe changes from convex to concave rapidly

• Insect further stimulates sensory hairs.

• More ca2+ influx → exocytosis of digestive enzymes.

• Complete closure of trap.

Adaptation of flytrap

• Stimulation of single hair not causing immediate closure, drop of water can do this = wasted energy.

• If lots of rain = doesnt completely close

• Doesnt completely close = tiny insects escape because not worth the energy compared to closing.

Gibberellins

• causes stem elongation

• Causes seed germination

Auxin process

• Auxin binds to auxin receptor

• Causes proton pump to actively pump H+ into cell wall.

• Acidifies cell wall

• Activates expansins which disrupt hydrogen bonds

• K+ and H2O rush into cell (increases internal pressure)

• cellulose microfibrils move further apart allowing cells to elongate.

Gibberellin function

• XET breaks bonds between hemicellulose

• Cellulose microfibrils move further apart

• Allows expansion of cell wall leading to cell elongation.

Seed structure

Gibberellin for seed germination

• H2O uptake by seed

• Embryo releases gibberellins.

• Gibberellins diffuse to aleurone layer

• Cells of aleurone layer synthesis amylase

• Amylase hydrolyses starch → maltose → glucose

• Embryo uses glucose to respire and grow

Gibberellin germination

Diploid cell def

The cell contains 2 sets of chromosomes

Haploid cell def

The cell contains 1 set of chromosomes

Homologous chromosomes

Pair of chromosomes of same length, positions of centromere, and same gene loci.

Meiosis 1

Seperation of homologous chromosomes

Meiosis 2

separation of sister chromatids

Why is meiosis reduction division

• halves no. of chromosomes in nucleus

• Changes a diploid cell to haploid cells.