Molecular Biology Notes

Table of contents
2.1 Metabolic molecules......................................................................................................................... 3
Main groups of Organic Compounds................................................................................................ 3
Why vitalism is incorrect...................................................................................................................4
Metabolism........................................................................................................................................ 4
2.2 Water................................................................................................................................................. 4
Structure of water.............................................................................................................................. 4
Properties of water.............................................................................................................................4
2.3 Carbohydrates + Lipids...................................................................................................................5
Polysaccharides................................................................................................................................. 5
Lipids................................................................................................................................................. 6
Types of fatty acids............................................................................................................................7
Triglycerides...................................................................................................................................... 8
Carbohydrates vs Lipids.................................................................................................................... 9
BMI....................................................................................................................................................9
2.4 Proteins............................................................................................................................................10
Amino Acids....................................................................................................................................10
Protein structure...............................................................................................................................10
Denaturation (Change or Loss of Protein Structure)....................................................................... 10
Genes and Polypeptides...................................................................................................................11
Proteome..........................................................................................................................................11
Different Functions of Proteins........................................................................................................11
2.5 Enzymes.......................................................................................................................................... 11
Factors That Affect Enzyme Activity.............................................................................................. 12
The Use of Enzymes For Industrial Practices................................................................................. 12
Lock and Key vs Induced Fit...........................................................................................................13
2.6 DNA and RNA Structure...............................................................................................................13
DNA Structure................................................................................................................................. 14
Watson and Crick Model................................................................................................................. 14
Types of RNA.................................................................................................................................. 14
2.7 Synthesis of Protein From DNA....................................................................................................15
Replication (DNA → more DNA)...................................................................................................15
Transcription (DNA → mRNA)...................................................................................................... 15
Translation (mRNA → amino acids, proteins and polypeptide chains).......................................... 16
2.8 Cellular Respiration.......................................................................................................................16
Anaerobic respiration...................................................................................................................... 17
Aerobic respiration.......................................................................................................................... 17
Application of fermentation.............................................................................................................17
2.9 Photosynthesis................................................................................................................................ 18
Chlorophyll......................................................................................................................................19
Light Dependent Reaction............................................................................................................... 19
Light Independent Reaction.............................................................................................................20
Chromatography.............................................................................................................................. 20
Limiting Factors of Photosynthesis................................................................................................. 20
Oxygenation of the Earth.................................................................................................................21
Structure of a Chloroplast................................................................................................................21
2.1 Metabolic molecules
Organic compounds contain carbon and are found in living organisms
- Exceptions: carbonates, carbides, carbon oxide (these contain carbon and are found in living
organisms but are not counted as organic compounds)
- Carbon can form large and complex molecules - it has the ability to participate in covalent
bonding
- The bonds between 2 carbon atoms are very strong / stable

Main groups of Organic Compounds

Carbohydrates
- Mainly function as a source of energy
- May be for recognition or structure
Building blocks of carbohydrates; monomers making monosaccharides. They are single sugars
- Needed skill: (glucose and ribose need to be drawn). Distinguish an α glucose and a β
glucose
Monosaccharides combine into disaccharides or polysaccharides. The type of bonding determines
what the polysaccharide is. eg) Glucose can combine to form glycogen or cellulose or starch.

Lipids
- Fats; non-polar hydrophobic molecules
- Main components of cell membranes
- Used as a long term energy storage
- Function as a signalling molecule
Most lipids have fatty acid chains as part of their overall structure - a long chain of hydrocarbons. If it
has a double bond it’s called an unsaturated fatty acid vice versa.
- Needed skills: Draw the general structure of a typical fatty acid.
Three types of lipids; simple lipids, compound lipid, derived lipids

Nucleic acids
- DNA and RNA - genetic material which controls protein synthesis etc
Monomers of a nucleic acid are nucleotides. Multiple nucleotides join together to form polynucleotide
chains. A nucleotide is formed with three things; phosphate group, pentose sugar, and the nitrogenous
base
- Needed skill: Draw a nucleotide
Polynucleotide chains can form a DNA double helix or RNA chain

Proteins
- All enzymes are proteins - important in speeding up or catalysing reactions
The monomer of a protein is an amino acid - when multiple amino acids combine they form
polypeptide chains. An amino acid has a central carbon and amine group (NH2), has a carboxyl group
(COOH), a variable R group
- Needed skills: Draw the general structure of an amino acid.
Why vitalism is incorrect
Vitalism is the idea that organic molecules Could only be synthesised by living organisms.
Historically, scientists believed that living things had a special force that created organic molecules.
This was disproved as scientists were able to artificially synthesise urea. Urea is an organic compound
as it’s a waste product of the body’s metabolism.
- They heated cyanic acid and ammonia which created urea

Metabolism
- All of the chemical processes that occur within a living organism in order to maintain life and
sustain itself etc.
- The sum of all the enzyme catalysed reactions that occur within an organism.
- Equal to anabolic reactions + catabolic reactions
- Two key roles:
- Provision of energy
- Synthesis or assimilation of materials for use within a cell
Anabolic reactions
- Takes simple molecules and builds them into more complex molecules
- Usually occur via condensation reactions - water is produced as a byproduct of the reaction.
These reactions generally expend energy
Catabolic reactions
- Takes complex molecules and breaks them down into simple molecules
- Normally occur through hydrolysis reactions - consumes or requires water
- Generally releases energy

2.2 Water

Structure of water
- Two hydrogen atoms which are covalently bonded
- Unequal electron distribution - water is a permanent dipole
- Because there is a charge difference water is polar
- Its polarity allows water to associate weakly with other polar molecules, or stronger bonds via
hydrogen bonding

Properties of water
Thermal properties
- Water can absorb or take on a lot of heat before it changes state → because the hydrogen
bonds are very strong
- Important; Internal conditions of an organism need to remain consistent →
homeostasis
- Can act as a coolant → sweat
Cohesion / adhesion
 - Cohesion; Water molecules will stick to each other due to the strength of hydrogen bonds
- Smaller organisms (especially unicellular) can move across the surface of the water
without it breaking
- Adhesion; Water will stick to other things
- Water needs to flow up the xylem, allows for organisms to move water in an anti
gravity matter
Universal solvency
- Polar + ionic substances dissolve easily into water
- Nutrients are able to be dissolved into water
- Blood → oxygen is dissolved into the blood
- Certain substances may be hydrophobic or hydrophilic and are able to be arranged
accordingly → phospholipids
- Acts as a mode of transport for nutrients etc

2.3 Carbohydrates + Lipids

- Monosaccharides; glucose, galactose, and fructose
- Monosaccharides are usually sweet and are normally an immediate energy source.
- Disaccharides (2 monosaccharides together); lactose, maltose, and sucrose
- Polysaccharides; cellulose, glycogen, and starch.
- Long term energy storage or cell structure

Polysaccharides
Cellulose Starch Glycogen

For structure Long term energy storage for Long term energy storage
plants

Found in the cell wall of plants Normally found in animals →

liver

Made of beta glucose Made of alpha glucose Made of alpha glucose

Generally indigestible for Comes in two forms Highly branched, more than
animals - Amylose amylopectin
- Linear
- Takes up less 1-4 linkages with additional
space 1-6 linkages
- Only 1-4
linkages
- Amylopectin
- Branched
- Easier to
digest + more
soluble
- 1-4 linkages
 with additional
1-6 linkages

Amylopectin:

Amylose

Homework: Draw a ribose and an alpha-glucose and beta-glucose and insert diagrams here

Lipids
Lipids can serve a diverse range of functions within a cell, including:

Storage of energy for long-term use (e.g. triglycerides)

Hormonal roles (e.g. steroids such as oestrogen and testosterone)
Insulation – both thermal (triglycerides) and electrical (sphingolipids)
Protection of internal organs (e.g. triglycerides and waxes)
Structural components of cells (e.g. phospholipids and cholesterol)

Types of Lipids

Triglycerides: Function as a long-term energy source in animals (fats) and plants (oils)
Phospholipids: Structural component of cell membranes
Steroids: Act as hormones in plants and animals, and is a structural component of animal cell
membranes (cholesterol)
Waxes: Act as a protective layer against water loss in plant leaves and animal skin
Carotenoids: Light-absorbing accessory pigment in plants (involved in photosynthesis)
Glycolipids: Complexes of carbohydrate and lipid that function as cell receptor and cell recognition
molecules

Types of fatty acids

Saturated Monounsaturated Polyunsaturated

Have no double bonds There is 1 double bond There is 2 or more double

- Between every carbon between 2 carbons at some
in the chain there is point in the chain
only a singular bond - Double bonds cause
- There is the maximum bends in the chain
number of hydrogen - Affects the capacity for
atoms for each carbon hydrogen atoms to
and in the chain attach to the carbon
- Monounsaturated +
polyunsaturated don’t
have the maximum
number of hydrogen
atoms for each carbon
in the chain
- Bent in 1 location
bonds between carbons at some
point in the chain
- Double bonds cause
bends in the chain
- Affects the capacity for
hydrogen atoms to
attach to the carbon
- Monounsaturated +
polyunsaturated don’t
have the maximum
number of hydrogen
atoms for each carbon
in the chain
- Bent in many
locations

Generally come from animal Normally come from plant Normally come from plant
sources. Normally solid at sources and will be liquid at sources and will be liquid at
room temperature room temperature eg) olive oil. room temperature eg) olive oil.
They can also be cis or trans They can also be cis or trans
- Cis - Cis
- Hydrogen - Hydrogen
atoms on atoms on
either side of either side of
the double the double
bond are on bond are on
the same side the same side
- Trans (do not naturally - Trans (do not naturally
occur, produced by occur, produced by
hydrogenation) hydrogenation)
- Hydrogen - Hydrogen
 atoms on atoms on
either side of either side of
the double the double
bond are on bond are on
opposite sides opposite sides
- Trans fats - Trans fats
restore the restore the
linear structure linear structure
and makes and makes
them a solid at them a solid at
room room
temperature temperature

Cis

Trans

Saturated fats increase LDL
levels within the body (i.e plant
oils in diet). Low density
lipoproteins (LDL) carry
cholesterol from the liver to the
rest of the body.
Unsaturated (cis) fats increase HDL levels within the body. High
density lipoproteins (HDL) scavenge excess cholesterol and carry
it back to the liver for disposal
Trans fats increase LDL levels and decrease HDL levels within
the body.

Saturated fat or trans fat dietary

intake (meat, butter, etc.)
generally correlates with higher
incidence of CHD, but not only
factor.

This is because increased

cholesterol in bloodstream
leads to atherosclerosis
(narrowing and blocking of the
vascular pathways).

Triglycerides
Most common form of lipids
- Used as long term energy storage in animals + plants
- Animals store their triglycerides as solid fats
- Plants store triglycerides as oil
Triglyceride is 3 fatty acid tails and a glycerol head. The hydroxyl group of the glycerol combines
with the carboxyl group of the fatty acids, an ester bond will be formed between carbon and oxygen
through a condensation reaction. The product of the condensation reaction is a triglyceride + 3
molecules of water.

Carbohydrates vs Lipids
Carbohydrates Lipids

Short term energy storage Long term energy storage

The ATP yield is less than lipids, about half as Per gram, stores about double in energy when
much compared to carbs

More readily and easily digested → can be used Difficult to break down a lipid → is only used
for both anaerobic and aerobic respiration for aerobic respiration

Have a greater effect on osmotic pressure → can Have less effect on osmotic pressure → can’t
dissolve in water dissolve in water

Easier to transport - soluble Difficult to transport - insoluble

BMI
Needed skills; calculate BMI using formula, know the categories, how to read a nomogram.
Formula; weight (kg) /height2 (m)
2.4 Proteins

Amino Acids
Homework: Draw a generalised amino acid
- There are 20 amino acids which are universal to all living organisms. There are a further 2
which are specific to certain organisms.
- Amino acids are joined together in the ribosome of a cell. When they are combined they form
polypeptide chains which then combine to form proteins. Different amino acids have different
chemical properties; polarity and charge.
- Amino acids join together using covalent bonds aka peptide bonds to form polypeptide
chains. They are bonded by a condensation reaction.

- The bonding of an amino acid is between the amine group and the carboxyl group. The amine
group loses hydrogen and the carboxylic acid loses a hydroxyl.

Protein structure
Primary structure
- The order of the amino acids → can affect how the polypeptide chain will fold
Secondary structure
- How the amino acid sequence folds; alpha helix (spiral / coil), beta pleated sheet (folded
staggered sheet)
Tertiary structure
- The 3D structure of the protein
- Fibrous or globular
- Fibrous; long, narrow and normally for structural purposes
- Globular; rounded, functional roles eg) enzymes etc
Quaternary structure
- Only applies to proteins that consist of multiple polypeptide chains linked together
- The way in which the multiple polypeptides are arranged and combined eg) haemoglobin

Denaturation (Change or Loss of Protein Structure)

Structural changes in protein that result in a loss or reduction of its biological function.
Most common causes:
Temperature
- High levels of temperature disrupt the hydrogen bonds that hold the protein together, as those
bonds break, the protein unfolds and loses shape, resulting in a loss of function.
pH
- Changing the pH will change the charge of the protein. This affects the protein's solubility and
shape. Each protein has their own optimal pH

Genes and Polypeptides

Genes in DNA code for what polypeptides will be produced. Typically 1 gene will encode for 1
polypeptide. Exceptions to this are; gene mutation, spliced genes etc.

Proteome
Proteome is the total set of proteins that can be created within a cell or organism. The proteome is
significantly larger than the genome.

Different Functions of Proteins

Structure
- Examples; collagen, spiders webs
Hormones
- Examples; insulin
Immunity
- Examples; antibodies
Transport
- Examples; haemoglobin
Sensation
- Examples; photoreceptor cells in the eye
Movement
- Examples; muscle fibres
Enzymes
- Examples; ligase

2.5 Enzymes
- Enzyme = globular protein, acts as a catalyst for chemical reactions
- They are reusable; the reaction they catalyse does not consume the enzyme
- Enzymes generally end in ase, the prefix relates to its functions eg the enzyme that breaks
down lipids is lipase
- Typically reactions occur in a water-based solution. The reactants (substrate) and enzymes are
floating randomly in the solution (Brownian motion)
 - There are certain scenarios in which enzymes are fixed in position (i.e proteins in
phospholipid bilayer)
- The active site is the point where the substrate will bind to the enzyme; they are typically
specific to the substrate (specificity)
- Having enzymes increases the probability that reactants will collide in a water-based solution
- When the enzyme and substrate bind it is called the enzyme-substrate complex

1. Enzymes and substrates are floating in aqueous solution. Enzyme and substrate fit according
to lock and key / induced fit model.
2. Enzyme and substrate bind, forming an enzyme substrate complex
3. Reaction is catalysed (can be anabolic or catabolic)
4. Products of the reaction detach from the enzyme, and the enzyme can be reused.

Factors That Affect Enzyme Activity

Temperature
- Too low: not enough thermal energy, reduced collision
- Optimum temperature
- Too high: denaturation
pH
- Too high or low = denaturation
Substrate concentration
- Positive correlation but plateaus once all active sites are occupied

- Required skill: explain effect at all stages for each factor and represent graphically

The Use of Enzymes For Industrial Practices

- Immobilise the enzymes by placing them on a static surface
- They can be used for food production, biofuel, medicine, biotechnology, making of paper and
certain textiles / types of cloth

Use of enzymes to break down lactose to create lactose free milk

- Lactose intolerance is particularly high in certain minority groups i.e Asian and African
- Lactase production in small intestine decreases as dietary intake of milk decreases
from childhood to adulthood, lactase is broken down by probiotic bacteria in large
intestine producing gas
- Lactose is a disaccharide made of glucose and galactose
- Lactase is attached to beads
- The milk is then passed through the milk like a filter multiple times until lactose is fully
broken down
- The lactase breaks down the lactose in the milk into glucose and galactose (which is why
lactose free milk is sweeter)
- Lactose free milk is appropriate for lactose intolerant individuals, it sweetens the milk without
using extra sugar and reduces the production time for cheese and yoghurt
Lock and Key vs Induced Fit
In most cases enzymes fit the lock and key method
- The enzyme has a perfect fit for the substrate and results in specificity
Some enzymes fit the induced fit
- The enzyme does not have a perfect fit but rather a rough fit
- When the enzyme and substrate form a complex the enzyme will undergo a conformational
change to create a perfect fit
- After the reaction the enzyme will return to its original shape
- This results in the enzymes having broad specificity; they can form complexes with a category
of substrates rather than 1 specific substrate

2.6 DNA and RNA Structure

- DNA and RNA are nucleic acids
- The monomer for a nucleic acid is a nucleotide
- Nucleotides are made of 3 things (from left to right); a phosphate group (circle), 5 carbon
pentose sugar (pentagon), nitrogenous bases (ATCG (U), rectangle)
- The phosphate group attaches to the 5’carbonn whereas the nitrogenous base attaches to the 1’
carbon

DNA RNA

More stable More versatile but less stable

Comes in a double helix Single stranded

Stores genetic information Transferring genetic information

Pentose sugar is deoxyribose (2’ carbon The pentose sugar is ribose (2’ carbon attached
attached only to H) to OH)

ATCG AUCG
DNA Structure
- Double helix composed of two antiparallel strands. They are linked by hydrogen bonds
between complementary base pairs
- A with T(2 hydrogen bonds) and C with G (3 hydrogen bonds)
- A and G are purines (pure As Gold) they are larger than pyrimidines
- T and C are pyrimidines
- Nucleotides are combined into 1 strand via condensation reactions; phosphodiester bond
- The phosphodiester bond is between the phosphate group and the hydroxyl group attached to
3’ carbon
- It forms a double helix because it is energy efficient and stable

Watson and Crick Model

Things that Watson and Crick already knew
- It had been proved already that DNA was made out of nucleotides
- In DNA there were equal numbers of purines and pyrimidines
- Rosalind Franklin produced a image of DNA that confirmed that DNA is helical

Through trial and error they discovered the current DNA model which possessed the following
qualities; antiparallel double helix, complementary base pairing, the outer edges of the bases remained
exposed.

Early Model Flaws:

- They tried a triple helix
- They tried to have the nitrogenous bases on the outside and the phosphate group of the inside
- Initially they didn’t have complementary base pairing

Types of RNA
mRNA, tRNA, rRNA

mRNA
- Messenger RNA
- A transcript or copy of DNA to eventually code for polypeptide production / protein synthesis
tRNA
- Transfer RNA
- The form in which the amino acids are transferred / carried to the organelle that’s responsible
for synthesis ie) ribosome.
rRNA
- Ribosomal RNA
- RNA that is a component of the ribosome. Ribosomes have their own genetic material
2.7 Synthesis of Protein From DNA

Replication (DNA → more DNA)

1) Helicase will unwind the double helix and separate the 2 strands by breaking down the
hydrogen bonds between the nitrogenous bases. This occurs at specific areas which are called
origin of replication. When they separate they create a replication fork; 2 strands running in
antiparallel direction.
2) DNA gyrase reduces the strain caused by the unwinding of DNA by relaxing the positive
supercoils via negative supercoiling.
3) SSB proteins bind to the separated DNA strands in order to prevent reannealing or being
digested. These proteins will get discarded once the template strand has been used.
4) DNA primase will generate a short RNA primer (a short sequence of nucleotides) and attach it
to the template strand. (starting point for DNA polymerase; DNA polymerase can extend a
nucleotide chain but cannot initiate them)
5) Free nucleotides will align opposite of their complementary base pairings.
6) DNA polymerase III will attach to the 3’ end of the RNA primer (step 4). Then the DNA
polymerase III will move in a 5’ to 3’ direction (can only move in this direction). It will
covalently join the nucleotides together.
7) Because DNA strands are antiparallel, the DNA polymerase III will move in opposite
directions on the 2 strands. The leading strand; 5’ to 3’, The lagging strand; 3’ to 5’. On the
leading strand, the DNA will move towards the replication fork and will be able to synthesise
continuously, whereas on the lagging strand it needs to move away from the replication fork
and therefore needs to synthesise in Okazaki fragments.
8) At the end, DNA ligase will join all the Okazaki fragments into one continuous strand
9) The result of this is two identical DNA molecules

DNA replication is a semi-conservative process that occurs in the nucleus, meaning one strand on each
DNA molecule created as a product is conserved from the original

DNA replication is industrially/artificially conducted through the polymerase chain reaction. This is
important for medical purposes or forensic purposes etc.
1) DNA sample is heated to break down the hydrogen bonds and separate it into 2 strands
2) Then it is cooled to allow for annealing
3) It’s heated again to the optimum temperature for TAQ polymerase which causes strands to
attach via complementary base pairing
4) Each PCR reaction doubles the amount of DNA (artificial DNA replication!)

Transcription (DNA → mRNA)

Turns DNA into RNA which will eventually tell the ribosome what protein to synthesise.

Genes
The section of DNA which is transcribed into mRnA is called a gene. A gene is made up of 3
components:
 1) Promoter Sequence; the promoter doesn’t encode for anything but it is a sequence of
nitrogenous bases that signal to initiate transcription and is the binding site for RNA
polymerase
2) The coding sequence; this is what gets transcribed, acts as the template for RNA being
synthesised
3) Terminator sequence; The sequence that tells RNA polymerase to stop.

Antisense vs. sense strand

The antisense strand is the template strand that will be transcribed into mRNA
The sense strand is not transcribed

Steps for Transcription (occurs in nucleus)

1) Initiation; RNA polymerase binds to the promoter and causes the DNA strand to unwind and
separate
2) Elongation; whilst the DNA strands are separated, free nucleotides will align opposite the
complementary base partners on the antisense (template) strand. Then the RNA polymerase
will move along the coding sequence in a 5’ to 3’ direction to synthesise RNA
3) Termination; once the RNA polymerase reaches the terminator sequence, the enzyme
detaches, the RNA also detaches and the DNA helix will reform

Translation (mRNA → amino acids, proteins and polypeptide chains)

1) Initiation; the small ribosomal subunit in the cytoplasm will attach to the 5’ end of the mRNA
and will move along the mRNA until it finds a start codon.
2) The appropriate tRNA molecule will bind to the start codon via its anticodon (i.e according to
complementary base pairing)
3) Each tRNA carries a specific amino acid
4) The ribosome will move along the mRNA and will form peptide bonds between the amino
acids of the tRNA it attaches. This causes a polypeptide chain to be formed until the ribosome
reaches a stop codon at which point the translation will stop and the polypeptide chain will be
released.

2.8 Cellular Respiration

C6H12O6 + 6O2 → 6CO2+6H2O+ATP
The controlled release of energy where organic compounds are broken down to produce ATP. Aerobic
respiration utilises oxygen which facilitates the complete breakdown of glucose within the
mitochondria, thus resulting in a larger ATP yield. In contrast, anaerobic respiration involves partial
breakdown of glucose because oxygen is inaccessible (occurs in the cytosol), resulting in a smaller
ATP yield.

ATP=Adenosine triphosphate
- It’s a high energy molecule which is immediately available as a source of energy in the cell
from cellular respiration
- Serves as the immediate energy source for all cellular processes
 - One molecule of ATP has 3 phosphate groups, these phosphate groups are covalently linked,
storing potential energy in the bond
- When ATP is hydrolyzed (broken down) into ADP+Pi, the energy in the bond is released

Anaerobic respiration
- Glycolysis occurs (this occurs first in both anaerobic and aerobic), glucose (6C) is broken
down into x2 pyruvate (3C)
- Glucose gets broken down ‘in half’
- 2ATP gets consumed during this process into 2ADP, in return 4ADP get turned into
4ATP meaning a total 2ATP yield
- 2NAD+ turns into NADH
- No further ATP is created due to lack of oxygen
- The pyruvate will either be converted into lactic acid (animals) or ethanol and carbon dioxide
(plants), in the presence of oxygen, lactic acid can be converted back into pyruvate
- Anaerobic respiration serves the purpose of replenishing stocks of NAD+ because it’s a fuel
for glycolysis, and also for providing energy when oxygen supply is inadequate
Application:
Exercise requires high power muscle contractions which therefore require high levels of APT, when
exercising at a high intensity, the cellular demands for ATP will exceed the amount of O2 available, as
a result the body resorts to using anaerobic respiration which will lead to a buildup of lactic acid
which causes muscular fatigue.

Aerobic respiration
Requires oxygen and takes place in the mitochondria.
- Glycolysis occurs (same manner as anaerobic respiration. It still yields the same end products
- The x2 pyruvate will go into the link reaction and will get converted into x2 acetylCoA (this
occurs in the matrix
- The acetyl CoA gets taken into the Kreb cycle and the result of the Kreb cycle is 2 ATP (1,
but happens twice)
- The NADH and FADH which is produced by the Kreb cycle will be used to determine the
gradient in the electron transport chain which creates a product of 32 ATP (occurs in the inner
membrane)
- The total net gain is 36

Application of fermentation
In plants and yeasts, the byproducts of anaerobic respiration are carbon dioxide and ethanol. The
industrial use of CO2 in anaerobic respiration can be used to raise things eg, bread, alcohol production.
Bacteria that produce lactic acid help to produce yoghurts and cheeses etc. The products of anaerobic
respiration are utilised in industrial processes.
Skill: using a respirometer. A respirometer is a device that determines an organism's rate of
respiration. It measures the exchange of O2 and CO2 in a closed environment which the living
specimen is sealed in. This can be done by; submerging the specimen in water and recording the pH,
or through a data logger, placing a CO2 absorbent within the experimental area and recording the
pressure using a manometer with water.

Factors affecting respiration rate: temperatures, age and activity, light levels or hydration (plants).

Extra points;
- In a standard explanation of cellular respiration, lipids and proteins can also be broken down,
however just mention glucose in responses

Anaerobic vs. Aerobic respiration

Anaerobic Aerobic

Initiated by glycolysis

Reactants; glucose Reactants; glucose + oxygen

Combustion is incomplete (breakdown of Combustion is complete (breakdown of glucose

glucose is incomplete) is complete)

Net yield is 2 Net yield is 36

Products; lactic acid, ethanol, carbon dioxide Products; carbon dioxide + water

Location: cytosol Location: cytosol and mitochondria

Stages: Glycolysis + Fermentation Stages: glycolysis, link reaction, Kreb cycle,

electron transport chain

2.9 Photosynthesis
The process by which cells synthesise organic compounds from inorganic molecules in the presence
of sunlight.
- Plant cells
- Certain bacteria
- Chlorophyll required

6CO2+12H2O(with light and chlorophyll) → C6H12O6+6O2+6H2O

Animals will consume these organic compounds as food and release the energy through cell
respiration. (cell resp and photosynthesis are catabolic and anabolic opposites)

- The electromagnetic spectrum is the range of all possible frequencies of electromagnetic

radiation. (i.e from microwaves all the way to x rays and gamma rays
 - Visible light / region of the spectrum is a component of the electromagnetic spectrum; this is
where the sun emits its peak power.
- The sun emits its power as white light which comes in 400-700 nanometers.
- Within white light is a range of colours which represent different wavelengths (rainbow
colours) red (700) → violet (400)

Chlorophyll
- Only certain colours are taken up by chlorophyll.
- Chlorophyll is a green pigment found in photosynthetic organisms which is the enabler for
light absorption.
- When chlorophyll absorbs light it releases electrons, which are important for ATP
synthesis.

- There are different types of chlorophyll which have different absorption spectrums
- Having different types of chlorophyll makes the cell more efficient at light absorption
- Group pigments together with different absorption spectra to minimise
wavelengths with little absorption
- This explains why not all plant leaves are green, and sometimes they can
change colour (i.e deciduous tree)
- In general chlorophyll absorbs blue and red, whereas green is the least absorbed/most
reflected, which is why leaves appear green.
- These pigments can have an absorption spectrum - a graph that has the amount of light
absorbed on the y-axis and the wavelengths of light on the x-axis.
- These pigments also can have an action spectrum
- Similar graph, which plots the level of photosynthesis at different wavelengths

- There is a high level of correlation between absorption and action, i.e more absorption means
more photosynthetic reaction

Light Dependent Reaction

The conversion of light energy into chemical energy
 - Light gets absorbed by the chlorophyll, resulting in the release of electrons which are then
used to synthesise ATP
- Photolysis: light is also absorbed by water which causes it to be split into hydrogen and
oxygen
- Hydrogen and ATP will be used for the light independent reactions and oxygen is released
from the stomata as a waste product

Light Independent Reaction

Chemical energy is used to synthesise organic compounds
- ATP and hydrogen from the light dependent reaction will be carried by NADPH and
transferred to the sight of the light independent reaction
- The site of the light independent reaction is the stroma (cytoplasm of the chloroplast
organelle)
- The hydrogen gets combined with CO2 and will be used to form complex organic compounds
- ATP provides the energy to power any reactions needed to fix those compounds together
(carbon fixation)

Chromatography
An experimental technique which is used to separate mixtures.
- Can be used to separate the different pigments used in photosynthesis

Mobile phase
- Mixture is dissolved in a fluid

Stationary phase
- Mixture is passed through a static material

Different components in the mixture will move at different speeds and will separate along whatever
the static material is. You can calculate an RF value (Distance component travelled)/(how far the
solvent travelled).
There are two types of techniques used to separate photosynthetic pigments;
- Paper chromatography
- Using paper (cellulose) as your stationary bed
- Thin layer chromatography
- Using a thin layer of absorbent (eg, silica gel)
- Generally this is faster and separates more clearly

Limiting Factors of Photosynthesis

Photosynthesis is dependent on a number of conditions that must be favourable;
- Temperature;
- Photosynthesis is controlled by enzymes
 - There is an optimum temperature - at too low a temperature there aren’t enough
collisions, at too high a temperature the enzymes denature.
- Light intensity;
- Light is necessary to be absorbed by chlorophyll to kickstart light dependent reaction
- Reaction rate will increase with light intensity as it means more chlorophyll are being
activated to produce ATP
- However, at a certain light intensity the rate will plateau
- It plateaus because the maximum chlorophyll will already be activated
- Light wavelengths (colour) can also have an effect on reaction rates
- Carbon dioxide concentration;
- The reactant of the light independent reaction
- It’s necessary to form organic molecules
- As CO2 concentration levels increase, the reaction rate will be higher because more
carbon fixation is occurring and more organic compounds are produced, however, at a
certain point, all the enzymes which help with carbon fixation will be occupied.

Chemical processes influenced by more than one condition will have their rate of reaction controlled
by the factor that is closest to its min. value

Oxygenation of the Earth

Biological photosynthesis is the only significant source of oxygen gas production.

Before plants, free oxygen was chemically captured and stored. After plants developed this ability,
they began to saturate earth with oxygen, leading to significant changes for:

- Oceans
- Initially, oceans had lots of dissolved iron from the crust, however when iron reacts
with O2 it forms an insoluble precipitate. Once all of the iron had reacted, oxygen
accumulated in the atmosphere
- Atmosphere
- Initially it was anoxic (oxygen-free), now it’s 22% oxygen in the atmosphere
- Rock deposition
- The same reaction between iron and oxygen led to banded iron formations - iron
oxide forming visible bands in rock
- Significant changes to biological life
- Certain anaerobic species were wiped out as oxygen was toxic to them, however, the
availability of free oxygen in the atmosphere led to the development of aerobic
respiring animals

Structure of a Chloroplast
(include a diagram; thylakoids, grana/granum, stroma, inner/outer membrane, lamella)
The chloroplast is the organelle responsible for photosynthesis and contains chlorophyll.