CELL BIOLOGY 2

MOLECULAR BIOLOGY 18
METABOLISM 30
CELLULAR RESPIRATION 34
PHOTOSYNTHESIS 36
DIGESTION AND ABSORPTION 39
THE BLOOD SYSTEM 47
ECOLOGY 52
CELL BIOLOGY
CELL THEORY
Outline
1. All living organisms are made up of cells
2. A cell performs all the functions necessary for life
3. Cells arise from pre existing cells

Cells of living organisms vary in their structure, but they have some common properties:
1. All contain genetic material
2. All are surrounded by a plasma membrane
3. All perform metabolic functions
4. All have a mechanism to produce energy

• The cell is considered to be the basic and smallest unit of life.

• Anything smaller is incapable of life.
• Living organisms can be unicellular (e.g. bacteria- protozoa/ yeast) or multicellular (e.g.
humans)
• Unicellular organisms carry out ALL the functions of life that are also seen in multicellular
organisms.

There are organisms that show exception to the cell theory, but most organisms fit. Because there
are exceptions it is a theory and not a law.

Exceptions

Striated muscles
• attached to bones
• has striations/bonds
• the cell is multi-nucleated (has many nuclei)

Giant algae / “Mermaid winde glass"/Acetabularia

• Algae are normally unicellular
• This plant has a single cell, which makes up the stalk and
goblet

Aseptate fungi (mushroom)

• The nonseptate hypha has no cross walls
• Multi-nucleated
METABOLIC ACTIVITIES
Performed by any single cell/living organism

gascous exchange
take in oxygen and give of CO2

locomotion movement

cellular respiration production of energy

reproduction e.g. cell devision

growth expansion through nutrition and C.R.

excretion removal of chemical waste of the body (only

urine)

irrability ability to be aware of ones surrounding and

reacting to it

1. ingestion
nutrition 2. digestion
3. absorbtion
4. egestion/ defaecation
5. excretion

Characteristics of a protozoan found in stagnant water (still water + fresh water)

1. unicellular
2. eukaryote (has nucleus)

Cell of paramecium (protozoan)

Suited to perform life functions because it has:
food vacuoles store food

micronucleus and reproduction

macronucleus
cilia movement

oral groove nutrition

anal pore nutrition

contractile vacuole
mitochondria C.R.

osmoregulation maintains water in

body; excretion

plasma membrane for gases exchange;

excretion; irritability;
sensitivity
 Cell Wall gives shape and
How a cell is suited to perform life activities protects

Starch • stores food

Subkingdom algae
• nutrition
Golgi apparatus transports substances
using vesicles

Mitochondrion responsible for C.R

Flagellum locomotion

Contractile vacuole osmoregulation and

excretion

Nucleus • reproduction
• controles metabolism
Endoplasmic reticulum • transports
substances inside the
cell
• nutrition
Vacuole gives turgidity and
stores water

Pyrenoid

Chloroplast • responsible for

photosynthesis
• nutrition
Plasma membrane • nutrition
• gaseous exchange
SURFACE AREA TO VOLUME RATIO • excretion

• As the volume of the cube increases, the

S.A./Vol. ratio decreased.
• The S.A/Vol. ratio affects the cuboidal cells
ability to carry out chemical processes.
The higher the ratio, the quicker the
chemical processes can be carried out.
When the S.A/Vol. ratio is low, the
substances and products more longer
distances to reach the center of the cell,
which makes the reactions slower and
therefore inefficient.
• Flat rectangles or flat spheres are the
shapes that allow the highest S.A/Vol. ratio
• If a cell becomes too big, it undergoes cell
devision to become flat again.

EMERGENT PROPERTIES
Cells are made up of organelles, which have different functions. This helps a cell in metabolism.
Each cell should be able to undergo C.R., nutrition extortion etc. The sum total of the functions
performed by a cell is more than the sum of the individual parts put together. In a multicellular
organism many cells work together to produce a much bigger result than the sum of all the cells
working e.g. human beings do not just perform the functions of metabolism. When the cells work
together, they are capable of producing higher order activities such as problem solving,
communication, emotion, intelligence, creativity , etc.
CELL DIFFERENTIATION AND SPECIALISATION
• Cells differentiate to increase the efficiency of the body
• They have to change their structure to suit the function, which they have to perform
When cells differentiate: they become groups of cells with the same structure and function
When cells specialise: they switch off certain genes and loose certain characteristics with that. The
switched on genes make certain proteins, which allow the cells to have certain functions.

STEM CELLS
Properties
1. Unspecialised
2. All genes are switched on
3. Capable of cell devision
4. Capable of differentiating into any type of cell (totipotent/pluripotent)
5. Found in all organs of the body
6. Stem cells can be harvested from the umbilical cord, blood, embryos and bone marrow.

Stem cells are responsible for the growth and development of the embryo.

specialisation
depends on
—> position of the
ovum —> Zygote —> Embryo cell in the
+ specialisation (to
(mitosis) (only stem
tissue, organs, embryo and on
sperm cells) the needs of the
systems etc.)
body

Therapeutic use of stem cells

Stargardt’s disease
• Genetic disease caused by mutation in a gene
• Condition is recessive
• Develops between 6 - 12 years
• Membrane protein needed for active transport in retinal cells malfunctions
• Photoreceptive retinal cells degenerate
• Vision impairment progresses
• One patient was treated with embryonic stencils
• Stem cells are injected into retina
• Cells differentiate into retinal cells
• Improved vision

Leukaemia

• Adult stem cells are extracted with a needle from bone marrow
• Stem cells are stored
• Patient is treated chemotherapeutic, which kills the cancerous white blood cells
• Stemm cells are inserted and replace killed blood cells
 Ethics of using stem cells for therapeutic purposes
Sources of stem cells:

Embryonic stem cell Before cells start to differentiate in the embryo, stem
cells are removed

Umbilical cord blood stem cell after the birth the babies blood is removed from the
umbilical cord and can be frozen until the person
dies

Adult stem cell Taken from bone marrow of a person that has to be
treated. A needle is pocked right into the bone and
the stem cells are extracted.

• Embryos are specially created in the lab for therapeutic purposes

• The moment the stem cells are extracted, the embryo is killed
• Is an early embryo stage as much a human as a new born baby? When does life begin?
• Does it begin with the formation of a zygote, when organs are formed, when the embryo can
actually feel or when it has become a foetus who can live outside the womb?

• IVF (Inviteral fertilisation - fertilisation outside of body) embryos are formed for the sake of
harvesting stem cells. They would not have existed otherwise.
• IVF involves hormone treatment of women and a surgery to remove eggs
• The eggs chosen are exploited of society
• However, the advantages of this are that heavily sick people can become healthy again

ULTRASTRUCTURE OF CELLS
The invention of electron microscopes led to greater understanding of cell structure

Structure of a prokaryotic cell

Flagellum solid

Pilus hollow cylinder transports plasmids

Cell wall permuable • protects against

mechanical energy
• turgerpressure

Plasma Membrane semi permuable • nutrition

• gaseous exchange
• excretion

Cytoplasm contains all raw

materials for
metabolism

Plasmids • extension to
nucleoid
• controls functions
and characteristics
of those
Cell • Globular/ovule cells
• no membrane-bond organelles Ribosomes
• found in large intestine
• can change its genetic material which Nucleoid has all the DNA
is why prokaryotes survived so long. controls metabolism
There is no genetic variety because by making certain
there is no sexual reproduction. protein which become
Plasmids can change and can become ´ enzymes that control
resistant against different things e.g. the speed of
antibiotics functions
 Electron micrograph of prokaryotic cell Prokaryotic cells divide by binary fission.

1. Cells replicate their DNA in the nucleoid and

plasmids
2. The replicated DNA separates
3. Cytoplasm divides
4. Cell Wall and Plasma Membrane are formed in
the middle of the cell
5. Cell divides

Structure of Eukaryotic cells

Exocrine
gland cell of pancreas -
Animal cell ! Plasma Membrane • semi permuable • nutrition
• microvilli allow P.M to • gaseous exchange
extend to increase S.A • excretion
Structure of a plant cell
Cytoplasm contains all raw
materials for metabolism

Vesicles transports special

substances (e.g.
modified enzymes/
proteins)

Polysomes (…) make protein used

locally (not
transported)

Centrosomes with attach to spindle

Centrioles fibres during cell
devision
Lysosome contain enzymes that
destroy non functional
parts of a cell or
bacteria

Mitochondrion Cellular Respiration

Cell • has different compartments and Endoplasmic transports substances

each of the compartment has a reticulum within the cytoplasm
different thing to full fill
(organelles) Ribosomes produce protein
• organelles either have a single or
a double membrane Golgi body • modifies and
packages materials
• advantages:
• substrates and enzymes are • transports substances
concentrated in a particular using vesicles
region • mainly protein
• lytic chemicals can be kept in Nucleus Nucleolus • carries genetic
membrane bond organelles Nuclear membrane material
• conditions (e.g. pH) can be Nuclear pores • controls all activities in
maintained for specific Genetic material the cell
reactions
• organelles can be moved
around the cell
 Cell • long, rectangular
Plasma Membrane • semi permuable • nutrition
Structure of a plant cell • microvilli allow P.M to • gaseous exchange
extend to increase S.A • excretion

Cytoplasm contains all raw

materials for metabolism

Mitochondrion Cellular Respiration

Endoplasmic transports substances

reticulum within the cytoplasm

Ribosomes produce protein

Golgi body • modifies and

packages materials
• transports substances
using vesicles
• mainly protein

Nucleus Nucleolus • carries genetic

Nuclear membrane material
Nuclear pores • controls all activities in
Genetic material the cell

Chloroplast

Vacuole

Electron Micrographs
 Prokaryotic Cell Eukaryotic Cell

has nucleoid has nucleus (surrounded by membrane)

no membrane bound organelles membrane bond organelles

plasmid no plasmid

small large

pilus no pilli

always cell wall may or may not have a cell wall

has 70s ribosome has 80s ribosome

genetic material is naked DNA DNA is associated with protein

genetic material is circular nucleoid genetic materials is linear chromosomes

Plant Cell Animal Cell

golgi body, mitochondria, nucleus, cytoplasm, plasma membrane, ribosomes, endoplasmic reticulum

cell wall no cell wall

rigid / angular shape spherical / flexible shape

large vesicles small vesicles

no microvilli microvilli

no lysosomes has lysosomes

no centrosome centrosome + centriole

MEMBRANE STRUCTURE
1920 - Gorter and Grendels model —> chemical analysis of The model is accepted by scientists for about 30 years. It was
plasma membrane showed that a bilayer of phospholipid is proved by:
present. Their model didn't speak about how the protein was 1. Freeze ethced electron micrograph
arranged 1. Rapid freezing and fracturing of cells
1930 - Davson and Danielli’s model —> two layers of 2. Phospholipic layers seperated+Globular structures
phospholipid sandwiched between two layers of protein. scattered in the membrane interpreted as
Supported by electron micrographs of plasma membrane that transmembrane protein
showed two dark lines with a ligher bond between. Dank bonds 3. showed irregular arrangement of protein
interpreted as protein and light bond as phospholipids. 2. Structure of membrane protein
1. Proteins extracted showed various sizes and shapes
1966 - Singer and Nicholson model —> 2. Not supported by Davson.Danielli model
showed that there was no regular 3. Hydrophobic sections of proteins suggested they were
arrangement of proteins and that these at least partly embedded in phospholipid
looked like tiles in a mosaic that occupied 3. Fluorescent antibody tagging
different position. Also the model showed 1. red or green fluorescent markers attached to
peripheral proteins on both sides of the antibodies
P.M. and that the integral protein are 2. antibodies with green marker allowed to bond with
demean and produced on one or both sides. During their proteins on another cell
research they found out, that the phospholipids are free to move 3. the two cells are allowed to fuse and left for 40
and that the proteins can therefore also move. This resulted in minutes
the fluid mosaic model. 4. the red and green markers were found mixed
throughout membrane
5. shows that proteins are mobile
Fluid mosaic model of Plasma Membrane
Properties of phospholipid leading to
the formation of the membrane bilayer

• ‘Heads’ contain phosphate groups

• They are hydrophilic (attract water),
therefore also polar
• They face the large water content of the
tissue fled and cytoplasm on opposite sides
of the membrane
•The fatty acid tails are non. charged,
hydrophobic and non polar (repel water)
• This combination creates a barrier between
the internal and external water environments
of the cell
• ‘Tails’ create a barrier to the movement of
charged molecules
•The individual phospholipids are attracted
through their charges, which gives some
stability
• They can however only move up and down but
not sideways
•The stability increases by the presence of
cholesterol molecules
•The whole structure is amphipathic, where on end
is hydrophilic and one end is hydrophobic
•The advantage of this is that polar substances
cant pass through because the tails are non polar
and therefore reject everything that is polar. This is
good because the cell doesn't ‘over flood’ or die
because of too much water. It can control how much comes in and out. The structure makes a barrier to
water.
• When phospholipids are placed in water they form stable bilayers, which is the basic structure of all
membranes +The structure prevents hydrophilic substances to pass through and from an effective barrier

Proteins on the plasma membrane can be classified based on structure, position in the membrane
and function
Structure and position of membrane proteins

Integral Protein Peripheral Protein

Position in membrane embedded in tails embedded on the head

Presence of hydrophilic part at the top and the bottom there is yes, part facing cytoplasm, where
a hydrophilic part facing the heads are
cytpüöa,s. tissue fluid and inside

Position of hydrophilic part in the part that is embedded in the no. most of the time no if yes the
membrane tail position would be embedded in
the tail

Presence of hydrophobic part

Position of hydrophobic part in

membrane
Function of membrane proteins

Type of Protein Function

Hormone receptor a molecule that can bind to a specific hormone. The receptors found
on the membrane are particularly made to bind peptides e.g. fatty
acids

Immobilised enzyme enzyme that is attached to an insoluble material. This can increase
the resistance to change the condition in pH or temperature

Cell adhesive The binding of a cell to a surface or substrate

Neuroreceptors receives chemical signals from outside of the cell causing cell to
respond to them e.g. adjusting electrical activity of cell

Channel Protein allows polar substances to pass through

Protein Pump transports big substances across the cell (active transport)

• High protein content in the membrane indicates an active cell because Carrier protein, Chanel
protein, protein pumps etc are responsible for carrying substances
• more protein = more enzymes = more reaction
• This is why Mitochondria and chloroplast are made up of protein up to 75%

Cholesterol
There is a small part of cholesterol that is hydrophilic, which is near the head whereas the rest of it
is hydrophobic and embedded in the tail region. It is a steroid and keeps the cell fluid and a bit firm.

How positioning of cholesterol is responsible for the characteristics and functions of the
plasma membrane
• Membrane is partly solid and partly fluid
• Phospholipid heads are solid and phospholipid tails are fluid
• Increased fluidity increases movement of substances in and out
• Decreased fluidity restricts movement
• Cholesterol prevents regular phospholipid arrangement that may result in crystallisation
(cholesterol breaks pattern of phospholipids which prevents them from crystallising)
• Presence of cholesterol reduces fluidity
• Reduces permeability to Hydrogen and Sodium ions

MEMBRANE TRANSPORT
Simple diffusion - Movement of substances from
high to low concentrations along the concentration
gradient (no enzymes involved, passive)
This movement occurs both ways.
1. If water is needed for C.R for instance, it moves
in
2. If the concentration gradient of CO2 is higher
inside the cell than outside because of C. R.
the CO2 moves out the same way
Facilitated diffusion - Movement of polar/ big
substances from high to low concentrations along
the concentration gradient with the usage of
energy

Osmosis - The movement of water from a region

of low solute concentration to high solute
concentration through a differentially permeable
membrane

Factors affecting diffusion and osmosis

temperature high high temperature increases rate

of enzymes and therefore the rate
low of diffusion, however if the
temperature is too high the
enzymes will denature and the
proteins will be destroyed. max.
45°C

size of particles large reduces diffusion rate

small increases diffusion rate

concentration gradient high increases diffusion rate

low reduces diffusion rate

surface area high increases diffusion rate

low reduces diffusion rate

Exosmosis and Endosmosis in plant cells

• Size of cell always

stays the same
because the CW
restricts growth
• When a cell looses
excessive water
through exosmosis and
the condition cant be
reversed it is called
plasmolysis

If a red blood cell is

When water moves in When cell looses water placed into distilled
e.g. plant put in salt water for 10 minutes…
water the burger pressure
increases and the P.M.
Cell is turgid Cell is plasid
breaks. Plat cells wouldn't
- ‘Normal’ stage - break because of the C.W
P.M. moves close to P.M. draws away from
CW CW which provides pressure
from the other side and
Vacuole gets larger Vacuole reduces forbids the breaking. Also
the CC:W will stop the
P.M of taking in more
water some time.
 Tissues and organs are used in medical procedures. They need to be stored in certain solutions
between transplants. Comment on the chemical nature of
these solutions.

Active transport - Movement of substances against the

concentration gradient involving energy and carrier protein or
a protein pump.

• The protein pump provides energy to let the reaction

happen
• Action potential: Na+ goes down, K+ goes up
• K+ gated channel, this only works if it changes (structure of
protein changes when ARP is added)
• Has a protein that blocks it all the time but when voltage
changes the protein goes away

Bulk transport - Movement of large solid particles or drops of liquid into or out of the cell by the
movement of the plasma membrane.

endocytosis endocytosis endocytosis endocytosis endocytosis / exocytosis

exocytosis

Bacterium Phagosome cyosome fuses Bacteria is Residual body

with phagosome surcreted and attaches to
and it becomes a vacuole becomes membrane and
food vacuole residual body membrane
releases the rest
of the bacteria

Animal Cell Plasma Membrane Heads touch again

surrounds and because
engulfs Bacterium hydrophilic (attract
each other)

Nucleus cyosome

The fluidity of the membrane allows it to change shape, break and and re-form during endocytosis
and exocytosis. The ‘heads’ attract each other as they are hydrophilic. The tails will align
themselves away from the heads as they are hydrophobic. The heads interlock, forming a
continuous layer in the region where the heads meet. The cholesterol between the tails increases
the stability of the membrane.

Vesicles are used to transport materials within a cell between the rough endoplasmic reticulum,
Golgi apparatus and plasma membrane If the material is liquid its called pinocytosis, if it is solid it
is called phagocytosis.
1. Fusion of membranes between Endoplasmic
Reticulum and vesicle
• when vesicle membrane fuses with E.R.
membrane it releases special substance to
E.R. to fuse with the protein
2. Membranes of E.R. break up into smaller units
—> Golgi apparatus
3. The membrane of the G.A. breaks up into
small vesicles
4. Vesicle membrane fuses with the plasma
membrane

Different types of transport across the membrane

Diffusion involves doesn't use energy Particles move e.g. Urea diffuses
phospholipids along the out of cell, oxygen
concentration diffuses in
gradient

Facilitated involves channel doesn't use energy Particles move e.g. movement of
diffusion protein along the glucose into the cell
concentration
gradient

Osmosis involves doesn't use energy Particles move e.g. water

phospholipids or along the
aqua porins concentration
(phospholipids that gradient of water
are very permeable
- made up of
protein=

Endocytosis involves uses ATP bulc movement e.g. phagocytosis

phospholipids or pinocytosis

Exocytosis involves uses ATP bulc movement e.g. secretion of

phospholipids saliva

Pumps involves carrier uses ATP Particles move e.g. sodium pumps,
protein and the against the potassium pumps
plasma membrane concentration etc.
gradient

Active Transport Passive Transport

requires ATP energy Doesn't require ATP energy

movement is against the conc. gradient movement is along the conc. gradient

involves protein carrier involves channel protein, phospholipids

involves polar and large substances involves non-polar and small particles

e.g. phagocytosis, sodium.potassium pump e.g. diffusion osmosis, facilitated diffusion

THE ORIGIN OF CELLS
Testing the general principles that underlie the natural world. the principle that cells only come from
pre-existing cells needs to be verified.

Components in living organisms are DNA/RNA, amino acids —> protein, sugar —> CO2.
However, these cant be made in the Lab. Scientists don't know how they were made and realised
that life didn’t start at a cell, it started at chemicals.

Theory (1) of spontaneous generation

Cells are formed by the division pre existing cells

Pasteurs experiment

Aim: wanted to dispose theory of spontaneous generation

Experiment:

Proved that: Living organisms will no spontaneous develop from non living matter

Theory 2
The cell formed from non-living material

Miller aud Urey experiment

M+U came up with an apparatus that was completely closed. They believed that in former times
there must have been a lot of urea, methane, ammonia, hydrogen and water vapour. So they let
the water vapour go through the apparatus and provided electric shocks to simulate storms and
lighting, which produced methane, ammonia etc. and thus life.

However, the conditions they thought of are unrealistic to some extent as it is not normal for
weather to thunder for weeks continuously.

Theory 3
The cell formed from the Polymerisation of carbon compounds

This theory says that the deep sea vents might have developed life. As the volcanoes under the
ocean release gases and steam, energy is given off. Carbon atoms like Amino Acids could have
developed to protein through polymerisation. Lipids could have been developed to membranes the
same way.

Theory 4
The cell formed from the membrane

Formation of membranes
Phospholipids and amphipathic compounds were formed once and produced bilayers. Vesicles
formed out of this leading to cells.

Theory 5
The cell formed by the mechanism of inheritance

The RNA had to exist first; and out of this the cell developed
Each individual has DNA, which is copied on RNA, which has the info to make Protein, which gives
the structure to from enzymes that forms functions.
Most properly the genetic material was RNA at the beginning because RNA has the info to make
protein, it can store information, it can replicate itself and it can act as a catalyst (makes protein).

Proof: in nature viruses can make copies of themselves by RNA

Endosymbiotic theory

• originally all cells were prokaryotes (vesicles with chemicals inside)

• some were anaerobes, produced energy without using O2
• some were heterotrophs, heterotrophic n nutrition (dependent on sth. else for food)
• during this time 2 cells were special
1. one of the cells must have developed a method of aerobic respiration
2. second one must have developed a method of making its own food (photosynthesis)
• a cell that couldn't to both took both cells inside
• one/some became autotrophic/photosynthetic
• one/some developed aerobic respiration
• mitochondria and chloroplast were prokaryotes that entered symbiotic relationship with a bigger
prokaryote
• natural selection let to this relationship becoming a eukaryotic cell

Evidence:
• own DNA
• 70s ribosome (indicates that they must have lived on their own some time during evolution,
normal eukaryotes have 80s ribosomes
• own transcription to make some proteins
• produced by devision of pre-existing mitochondria or chloroplasts

CELL DEVISION - MITOSIS

Serendipity and scientific discoveries - the discovery of cyclins was accidental

Mitosis results in the nucleus dividing into two genetically identical nuclei. The DNA replicates two
copies. The Copies move to opposite sides of the cell and the cytoplasm splits. Two identical cells
are created.

Mitosis is responsible for the following

functions in living organisms:
• growth
• replacing dead/injured tissue/cells
• asexual reproduction
• growth and development of the embryo
The stages in the cell cycle

The stage of mitosis can also be called

karyokinesis, which means the devision of
the nucleus. The whole cell cycle can be
divided into interphase and mitosis. The
major part of the cell cycle comprises the
interphase. This stage is divided into G1, S
and G2 phases. During the G1 phase, the organelles replicate, cells grow, all metabolic functions
are performed. During the S phase DNA replicates. However, not all cells go through the S phase.
Some grow and specialise immediately, we call the G0. During the G2 phase, all the enzymes and
 materials for the devision of every organelle are made. Interphase is an active phase in the cell
during which many metabolic activities take place including C.R, photosynthesis, nutrition, growth
etc.

Cyclins, a group of chemicals that control different stages to the cell cycle, bind to cyclin dependent
kinases. Kinases are enzymes responsible for karyokinesis, so for cell devision. When the cyclins
bind to them, they become active and attach phosphates to inactive enzymes to make them active
through providing the enzymes with activation energy. The active enzymes are then responsible to
control certain reactions in different stages of cell devision.

Stages in Mitosis

Prophase Metaphase Anaphase Telophase Cytokinesis

1. spindle fibres/ 1. The nuclear 1. The centromeres 1. All chromosomes Animal Cell Plant Cell
spindle membrane has have dividd and have reached the
microtubules broken down and the chromatids poles and
(made up of chromosomes have become nuclear 1. The plasma 1. vesicles align
protein) are have moved to chromosomes membranes form membrane at the themselves
growing the equator 2. Spindle around them equator is pulled between the two
2. Each 2. Spindle fibres microtubules pull 2. Spindle inwards until it nuclei
chromosome from both poles the genetically microtubules meets in the 2. they fuse to
consists of two are attached to identical break down centre of the cell become the
identical each centromere chromosomes to 3. Chromosomes 2. This divides the middle lamella
chromatids on opposite opposite poles uncoil and are no cell into two which extends
formed by DNA sides. longer and decides the
replication in 3. The spindle individually cell into two
interphase and fibres move visible 3. each cell
held together by chromosomes so deposits material
a centromere that they are on the cell plate
3. Spindle fibres aligned on the to form a cell wall
extend from each equatorial line to 4. the plasma
pole to the split membrane is
equator then played over
the cell wall
5. This divides the
cell into two
Cell devision is a controlled process. Cell division is controlled by genes called oncogene. Certain
chemicals or rations can cause changes in these genes that result in mutation and the agents that
cause these changes are called mutagens. These mutagens are also called carcinogens because
mutations of the oncogenes result in cancer.

Uncontrolled cell devision results in a mass of stem cells called a tumour. If the cells stay together,
do not invade neighbouring tissues or spread to other pars of the body, the tumour is termed
harmless or being.

If the cells of the tumour invade neighbouring tissues or detach and move to other parts of the
body, it is termed metastasis.

Cancer causing agents may be viruses, chemicals or radiations such as C rays and UV rays.

The first ball of cells formed as a result of an uncontrolled cell devision in the body is a primary
tumour. The additional ball of cells formed as a result of cells moving out of the primary tumour and
undergoing uncontrolled cell devision is the secondary tumour.

There is a positive correlation between caner and smoking. The smoke only passes through the
mouth, the pharynx, the larynx but also reaches the oesophagus, the stomach, the kidney, the
bladder, the pancreas and the cervix through blood transport. The more you smoke, the more
cancer you get. Cigarette smoke contains about 60 types of chemicals which are carcinogenic.
Even though the death rates are similar between smokers and non smokers, the chances are
higher in smokers to get cancer as with non smokers. This correlation does not signify a cause as
it is possible that cigarette smoke doesn't cause cancer, however smokers often do. As proof,
scientists tested 20 of the chemicals found in cigarettes on animals in the lab and all animal go
tumour.

MOLECULAR BIOLOGY
The discovery of nucleic acids and their role in protein synthesis and controlling characteristics of
living organisms led to the development of a new field called Molecular Biology. A molecular
biologist studies the chemical processes that occur in a cell and is able to explain how it is related
to metabolism.

Inorganic substances are small and simple in structure and include water, oxygen, carbon dioxide,
mixerals etc. Organic substances are very complex and large and include carbohydrates, protein,
lipids and nucleic acieds.

CHemical substances in the protoplasm are substrates for chemical reactions that sustain life. For
example Glucose and oxygen present in protoplasm react to release energy and form the waste
products water and carbon dioxide. This chemical process is the basis of the metabolic reaction
called cellular respiration.

This chapter is devoted to learning about the chemical reactions in the protoplasm that constitute
metabolism.

Many organic molecules present in the protoplasm can be synthesised in the lab. e.g. urea.

The theory of Vitalsm was used to explain how life occurs and how it originated. The theory of
vitalism states that living organisms have a vital principle which allows them to perform life
functions which are very different from physical and chemical forces occurring in nature. E.g. in the
lab we mix H2O +C02 to get water with gas. In the nature/ in a plant when H2p + Co2 combine, a
fruit will come out. We cannot produce a fruit because we cannot name glucose or proetins. We
get if from food.

1953 DNA was discovered. DNA is proteins with specific characteristics. When the body has too
much protein, it turns into urea and then glucose.

Urea is Co2 + NH3 —>

Because DNA/ Glucose

cant be made in the Lab, scientists proofed the theory with because urea could only be made by
living organisms

However, another scientist put silverisocyanate + NH4Cl and got urea.

He created urea in the lab and disproved the theory of vitalism . Therefore, the chemical and
physical reactions that take place in our body re quite similar to the ones happening in nature.

However, there is a difference in the urea produced in the lab and the one produced by the body.
One is a product from metabolism and the other from the lab. One uses catalysts from the lab and
the other enzymes from the body to mix urea.

The reductions view of life that states that life is made up of many chemical reactions taking place
in the cell and all the attributes of life can be related to chemical reactions. However, this is very
debatable as our common sense tells us that emergent properties are also vital for
life.

STRUCTURE OF A CARBON ATOM ionic bond -

when electrons
are transferred

covalent bond -
when electrons
are shared

electronic configuration
Carbon is an interesting atom that can form
single, double or triple bonds with other carbon
atoms. All bonds are however covalent.

Saturated compounds have single bonds between carbon atoms while unsaturated compounds
have double bonds between carbon atoms. Single bonds are more stable and less easier to break
than double bonds.

fatty acids saturated saturated

Living organisms are made up of cells. Protoplasm is the living material of a cell that is made up
of non living chemicals. Theses chemicals my be inorganic or organic. Inorganic substances are
small and simple in structure and include water, oxygen, carbon dioxide, minerals , etc. Organic
substances are very complex and large and include carbohydrates, proteins, lipids and nucleic
acids.

Inorganic and organic molecules in living organisms are composed of four main elements carbon,
hydrogen, oxygen and nitrogen. The other elements which are also important in living organisms
are calcium,. Potassium, iron, phosphorous,, and sodium. Sulphur, magnesium atoms etc. are also
elements that come across living organisms but are not as important. Life processes involve
important organic molecules such as carbohydrates, proteins, lipids and nuclei acids.

Metabolism refers to all chemical reactions taking place in the cell/body. All chemical reactions in
the cell require specific enzymes (protein that speeds up the reaction).

Anabolism refers to all reactions involving making complex substances to simple ones. E.g.
Photosynthesis: glucose becoming glycogen; condensation reaction.

Catabolism refers to all reactions involving complex substances becoming simple ones. E.g.
Cellular respiration, hydrolysis reactions; all reactions involved in digestion.

Hydrolysis Condensation

Water is a reactant Water is a product

Beaks down substances Builds up substances

Maltose + H2O —> 2 glucose glucose + glucose —> maltose + H2O

Protein + H2O —> many amino acids amino acids —> protein + H2O

WATER
Water is described as a polar molecule which means that the
molecule is charged. Water is charged because the shared electrons
are pulled closer to the oxygen. Through this oxygen is charged
negative and the hydrogens are charged slightly positive.

Properties of Water under Hydrogen bonding

In water molecules there is hydrogen bonding, which brings
molecules close to each other. When you supply the energy, it is used
to break down the hydrogen bonds between the molecules. This takes longer, which is why oil for
example heats up faster. In oil the energy was directly used to heat the molecules instead of
breaking the bonds first and then heating them.

Also, molecules in water don't have a lot of energy to move around as fast as the molecules from
oil, which is why old also reaches a higher temperature than water does. The specific heat capacity
of oil is lower that of water.

In nature this is good because the water in which the animals live in doesn't overheat with the suns
energy. Same way opposite, as the oil cools down much faster, water also takes longer to from
hydrogen bonds for the water to cool down. The change in water is mostly 1 - 3°C whereas the
changing temperature in the air is about 15°C.
Heating up water - we cool our body by sweating. The energy of the skin (heat) is used to break
down the hydrogen bonds. Afterwards, water evaporates. The heat is used to break the bonds =
the heat is lost. This is called high latent heat of vaporisation and sweating is an example of the
use of water as a coolant. When we sweat, we loose a lot of heat but little water, which keeps us
from drying out. If our body would use oil instead of water, it wouldn’t cool down as fast because of
the missing Hydrogen bonds. To have the same outcome our body would use more oil to sweat
and it would take longer.

Freezing water - water molecules get closer to each other when it is cooling down. This decreases
the volume nut increases the density. The lowest temperature you can get in water is about 4°C.
Below that, the top layer will freeze leaving water inside which is necessary for the animals to
survive. The water underneath the ice layer will not freeze because too much heat for that to occur
is trapped inside the hydrogen bonding.

Covalent bond Hydrogen bond

shares electrons intermolecular force (can hold two molecules

together)

strong weak

can occur between two non metallic atoms of the occurs between two molecules
same molecule

Thermal properties of water

Formula CH4 H2O Comparing the thermal properties of water and

methane
Molecular Mass 16 18

Density 0.46 g/cm3 1 g/cm3 All in all, water needs more energy than
methane to be broken/warmed up/cooled
Specific Heat 2.2 J/g/°C 4.2 J/g/°C down , etc., because of the hydrogen bonds.
Capacity

Latent Heat of 760 J/g 2.257 J/g Cohesive and adhesive properties
Vaporisation
This image shows how the cohesion of the
Melting Point - 182 °C - 100 °C water molecules at the interface of air and
Boiling Point - 160°C - 100 °C water has enough structural strength to
support the mass of an insect. The insect has
Physical State gas liquid exploited this nice opportunity through the
at Room evolution of structures and adapted to improve
Temperature its ability to move on the surface of the water.

Cohesion is the force of attraction between

water molecules. Adhesion is the force of
attraction between water molecules and
other polar substances. Surface tension is
an increased attraction of molecules at the
surface of a liquid resulting from forces of
attraction n fewer sides of the molecules.

Cohesion is important for water transport in

plants. Adhesion is useful in leaves when
water moves to cellulose molecules in cell
walls. This keeps walls moist so they can absorb carbon dioxide —> photosynthesis.
Solvent Property

Polar molecules dissolve in water because of hydrogen bonding between the solute and water.
Polar molecules dissociate in water and get surrounded by water molecules forming shells. Theses
shells prevent clumping together and keep the solute in solution. Water is therefore a medium in
which chemical reactions take place.

Hydrophilic and hydrophobic substances

Polar molecules are called hydrophilic because they are attracted to water. They can be easily
transported by water.

Fats and oils are hydrophobic molecules because they are not attracted to water. They are non
polar and tend to clump together in water. Theses are called hydrophobic interactions.

The solubility and mode of transport of these substances

Substance Polarity Solubility How it is transported

Glucose Polar High

Amino Acids Polar High

Cholesterol Non Polar Low Lipoproteins

Fats Non Polar Low Lipoproteins

Oxygen Non Polar Low Blood

Sodium Chloride Polar High

CARBOHYDRATES, LIPIDS AND PROTEINS

Organic compounds are made up of single units or many units joined together. These single units
are called monomers. They react with each other and form dimers, trimmers etc, or polymers.
When two monomers bond, they release one molecule of water. These synthesis reactions are
hence called condensation reactions. In the same way, a
dimer or polymer can be split into monomers with the addition of
water. This reaction is called hydrolysis reaction.

Sugar (monosaccharide) : a ring structure with oxygen forming

bonds between two carbon atoms. It has many OH groups. The
type of sugar depends on the number of carbon atoms. 5C is
ribose and 6C is glucose.

Fatty acid : a straight chain with many carbon atoms. It may

have single or double bonds between the Carbon atoms. It has
COOH (carboxyl) as a functional group.

Amino acid : It is a straight chain compound with many

carbon atoms. One end both the carbon chain has an amine
group (NH2) and the opposite end has a carboxyl (COOH)
group.
Carbohydrates

Carbohydrates are molecules made up of Carbon, Hydrogen and Oxygen. The Hydrogen and
oxygen are always in the ration 2:1 which si the same as in water, hence the mane carbohydrate.

Type Monosaccharide Disaccharide Polysaccharide

Number of Monomers

Examples • glucose (C6H12O6) • Maltose (C12H22O11) • starch

• ribose (C5H10O5) • Sucrose (Fr + Gl) • cellulose
• furctose • Lactose (milk/sugar) • glycogen (stored in
• galgactose liver and muscles)
• deoxyribose
(C5H10O4)

Condensation reaction

Monosaccharide + Monosaccharide —-> Disaccharide + Water

Glucose + Glucose —> Maltose + Water

C6H12O6 + C6H12O —> C12H22O11 + H2O

The same reaction in the reverse direction will be a hydrolysis reaction.

C12H22O11 + H2O —> C6H12O6 + C6H12O

Many monosaccharides link together to form polysaccharides such as cellulose, starch and
glycogen.

Comparison of structure and function of cellulose, starch and glycogen

Type of Cellulose Starch Glycogen
polysaccharide

Amylose Amylopectin

Monomer

Carbon atoms C1 and C4 bond without flipping

involved in
bonding

Shape of straight chain curved because of veil no fixed size

molecule

Branched/ no branching branching, all 6C • more branching

Unbranched face one direction then amylopectin
• more compact
Properties • found in the cell osmotically inactive(insoluble in water but • easy to
wall hydrophilic) metabolise
• tensile (forms • doesn't have
microphibroles = fixed size
many cellulose • made from
together) glucose

Function • gives shape of • stores glucose as reserve energy reserves energy for
cell wall • converts glucose to starch because CR
• withstands truer starch is osmotically inactive. Used as
pressure an energy reserve in plants, seeds and
• supplies water storage organs. Also temporarily stored
in leafs during photosynthesis.

Use/Importance • gives shape to • converts glucose to starch to store • found in animals

the cell wall and reserve energy in plants/seeds etc, • made from
is tensile against • is osmotically inactive glucose
burger pressure • reserves energy
• supplies cell with for CR
water • easier to
metabolise
• it doesn't have a
fixed shape

PROTEINS
Amino Acids

A straight chain compound with many Carbon atoms. One end of the carbon chain has an amine
group and the opposite end has a carboxyl group.

General structure:

The difference in the R group is what fives rise to the

variety of amine acids. R groups may be
hydrophilic or hydrophobic.

Amino acids link together by condensation

reactions.
There are 20 different types of amino acids in living organisms due to the 20 different R groups.
However, some organisms may have others, which are modified ones of the original 20.

E.g. Proline is an amino acid found on the protein collagen. In some positions, this is modified to
hydroxyproline, which increases the stability of the molecule

Amino acids and Polypeptides

Amino acids are linked together on ends of cells. The R groups and carbons of amino acids give
rise to a wide range of polypeptides in different organisms

The variety of tripeptides (containing 3 amino acids) possible with 20 amino acids is 20 x 20 x 20 0
203. A polypeptide may range from 20 to thousands of amino acids long. The variety of
polypeptides possible for a particular number of amino acids is = 20n where n = number of amino
acids.

Polypeptides and genes

The amino acid sequence of polypeptides is coded for by genes. The information is stored in the
form of a bace sequence on DNA. Each amino acid is coded by a sequence of 3 bases called
codon. This is called the triplet code.

Not all the information stored in the genes is for the sequence of amino acids in polypeptides.
Genes also control other functions.

Polypeptides and proteins

Polypeptides get folded to form three dimensional structures called proteins. A protein may be
made up of one or more polypeptides linked together. Insulin has two polypeptides, haemoglobin
has four.

Protein conformation
The conformation of a protein is its 3-dimensional structure. The shape of a protein will depend on
the amino acids sequence and the constant polypeptides

There are four levels of protein structure.

Primary structure • Made up out of amino acids
linked to each other
• The sequence and number of
animo acids determine what the
polypeptidee is
• Flat, peptide bonds
• Flipped amino acids
Secondary structure • hydrogen bonding Alpha Helix
• open loops
• areas where there are only
polypeptides
• from/are active sights of
enzymes
• curved, helix, alpha
• carbon bonds wit nitrogen
downwards
 • hydrogen bonding Beta pleated sheets
• flat sheets, poeta
• amino acid chain goes one way,
then turns around and goes the
other way
• the hydrogen bonds with the
oxygen

• include alpha helix and beta Open loops

sheets
• open loops connect them
Tertiary structure • To form a tertiary structure
between R groups of different
amino acids (on the same
polypeptide) chemical reactions
occur
• Two sulphides bond together
forming a disulphide bridge
which turns into a tertiary
structure through chemical
bonding between R groups

Quartenary structure • More than one polypeptide

• e.g. haemoglobin (4
polypeptides)
• globular structure

Protein Firbous Globular

Shape chain compact/ round

Solubility in water insoluable soluable

Nature of amino acids hydrophobic hydrophillic

Protein structure all R groups face one directions globular

—>Chain

Number of strands three three

Function

Structure related to function

Polar and non polar amino acids in protein structures

Polar and non polar amino acids can be found in the channel protein. Proteins are embedded in
the plasma membrane and have hydrophilic amino acids in the hydrophobic region of the
membrane. The polar amino acids face the inside of the channel protein and the outside and inside
of the cell.
Picture

Conjugated protein - made up of protein and non-protein (e.g. iron or magnesium found in
chlorophyl and haemoglobin) parts

Prosthetic groups - non protein part of conducted protein

Denaturation - when a protein changes its structure and looses its properties and function. This
can happen through e.g. changes in the pH or heating e.g. frying egg —> turns white

Functions of proteins

Protein Description Function

Rubisco • found in plants leaves • processes photosynthesis

• ribulose is the phosphate • breaks up RaBP so that it can
• carboxylase bond with CO2 to make glucose

Insulin • globular protein • has bonding site on the plasma

• hormone membrane and absorbs glucose
into cells
• reduces sugar level in the blood
Immunoglobulin • antibody • destroys antigen
• the chemicals that we take
into our body are called
antigen. The body produces
antibodies that destroy
antigen (the foreign
substances that enter our
body)
• Antibodies are produced by
many white blood cells to the
immune response

Rhodopsin • pigments found in the eye • changes shape of caught light of

• in red blood cells opsin

Collagen • made up of three proteins • allows strength and limited

• insoluble in water stretch
• most abundant protein in human
body
• found as mesh of fires in the
skin and walls of blood vessels
from ligaments and tendons

Spider silk • spiders use it to weave their • allows spider webs to suspend
webs animal and cattily prey
• strands of polypeptides are • linked to beta pleated sheet
linked to beta pleated sheet crystals adding to strength
crystals which add to strength

Proteome
A proteome is all the parts produced by a cell, tissue or organism. To determine the proteome,
protein mixtures are extracted from a sample and gel electrophoresis is done. This separates the
proteins, To identify the presence of a protein, antibodies for that protein with fluorescent markers
are used. The protein will fluorescent if present.

Each cell and individual has a unique protein, which can change over time. Even the proteome of
identical things can change with age.

Genomes are fixed but proteomes are variable.

Different genes = different protein, gender, age, conditions that cells are exported to etc. make
proteomes of an individual unique.
ENZYMES
A protein that speeds up chemical reactions and is produced in living organisms.
Characteristics:
• Globular protein
• Biological catalyst
• work intra and extra cellular
• catalyses only one biochemical reaction (substrate specific)
• has an active site (never used up; takes part in a reaction; needed in very small
quantities; can be reused)

The role of the active site of

an enzyme

• The active site is made up

of open loops from the
secondary structure
• positions the substrate in
such a way that bonds can
be made or broken

An enzyme-catalysed
reaction
A+B —enzyme—> C+D
glucose + glucose —enzyme—> carbose + H2O

•When molecules collide, they react

•to make them collide you have to give them
activation energy
•enzymes provide an active site where the
reactors can bond by using the activation energy

The higher the temperature is, the more

energy is supplied. Enzymes and substrate
collide more faster and the chances on both
colliding is higher, the rate of reaction in
creases. However, if the temperature gets too
high and the enzyme denatures there is no
more active site. If human have fever, the
metabolism stops too because of the
denaturing of the enzymes and the sweating
tries to bring body temperature down.

a) is the substrate because the concentration goes

down as the reaction proceeds
b) is the product because it increases as temperature
and the rate of the reaction increases
c) is the optimum temperature as enzymes work the
best at 37°C
d)…
 The higher the temperature is, the more energy is
supplied. Enzymes and substrate collide more faster and
the chances on both colliding is higher, the rate of
reaction in creases. However, if the temperature gets too
high and the enzyme denatures there is no more active
site. If human have fever, the metabolism stops too
because of the denaturing of the enzymes and the
sweating tries to bring body temperature down.

Effect of Temperature: the

higher the temperature, the
higher the rate of the reactions.
At a particular point, the rate
drops. The reason why it
increases, is because more
energy is supplied to enzymes
and substrates so they collide.
After a certain temperature
point however, the enzyme
denatures and the active size
no longer exists which is why
the reaction stops.

Effect of pH: Each enzyme

has its optimum pH. The pH
ranges at which an enzyme
works is narrow e.g. between 1 and 3, 5 and 6, etc.). Normal cellular enzymes have a pH of
about 7.2. Depending on where the enzyme works, the pH differs. Pepsin works in the
stomach because it is more acidic, salivary works in the mouth and is slightly alkaline
because it neutralises food and the acid that bacteria produce when decomposing food in
the mouth.

Effect of substrate concentration: When the substrate concentration is increased, the

rate of the reaction increases because there are more reactants/substrates/raw material to
react with. After a certain stage it plateaus because it reaches its max. and it cant go
beyond because of limited enzymes and active sites. There is no more place for the
reactants to happen. The hight of the reaction, so the maximum enzyme activity is
determined by the time where all enzymes are occupied, swell as all the active sites.

Denaturing
When the shape and structure of an enzyme change, it wont be able to function anymore.
When it gets denatured, the active site looses its shape and the substrate will no longer fit.
Enzymes are very sensitive e.g. optimum temperature lies between only 25°C and 35°C.

If hydrogen bonds break and the amino acids move further apart, polypeptides move away
from each other and the alpha helix and beta pleated sheets are lost.
Industrial use of enzymes

The use of lactase in the production of lactose free milk

Lactose is a disaccharide (glucose + galactose) milk sugar. Around 90% of all humans
show some kind of lactose intolerance. People who are lactose intolerant can drink milk if it
is lactose free. Lactase is an enzyme extracted form a yeast that can digest the milk sugar
to glucose and galactose.

Enzyme Immobilisation
It is possible to make the process more efficient by
immobilising the lactose on a recoverable surface
such as alginate.
1. First the Lactase is immobilized in alginate
beads.
2. Next the beads are placed in a container
over which milk can be passed.
3. The milk is collected and re-circulated
(pump) to convert any remaining lactose to
glucose and galactose.
4. The circulation is maintained until all
lactose has been converted.
5. This model of an industrial process allows
the lactase to be recovered and re-used
(cheaper).
6. Efficient conversion of lactose to glucose
and galactose.
7. Reduced purification of milk since enzyme
is retained and a high % lactose conversion
is achieved.
8. All these factors reduce cost particularly on
the downstream processing and
purification.

The advantages of immobilised enzymes are that

• the removed enzymes can be reused

The advantages of lactose free milk:

• ideal for lactose intolerant peoples
• prevents bloatedness, flatonlence
• texture is smoother
• other products require less sugar as the concentration of sugar doubles in lactose free
milk

METABOLISM
Metabolic reactions are regulated in response to the cell’s needs. The sum total of all chemical
reactions taking place in a living organism is referred to as metabolism. Metabolic reactions are
of two types anabolic and catabolic reactions. A metabolic reaction in a living organism often
occurs with a number of intermediary stages that are jointly referred to as a metabolic pathway.
Each stage has its own enzyme.
Metabolic pathways may either be a chain or a cyclic pathway of enzyme catalysed reactions.
Catabolic pathways involve the breaking down of complex molecules into simpler ones. Eg
C.R
Anabolic pathways involve the building up of complex molecules from simple ones. Eg
photosynthesis (any synthesis)
Chain Pathways
Enzyme (1) is specific to substrate 1.
Substrate 1 is changed to product 1.
Enzyme (2) is specific to substrate 2 which is also
Product 1 and is converted to product 2.
Enzyme 3 is specific to substrate 3 which is
also product 2 and is converted to product 3.
Product 3 is called the 'End product'.
e.g. Glycolysis

Cyclic Pathways
The initial substrate is fed into the cycle.
Enzyme (1) combines the regenerated intermediate 4 with
the initial substrate to catalyse the production of
intermediate 1.
Enzyme (2) is specific to intermediate 1
and converts intermediate 1 to
intermediate 2.
Enzyme 2 is specific to intermediate 2
and catalyses its conversion to intermediate 3.
The product leaves the reaction while intermediate 3
carries on with the cycle.
Enzyme (4) is specific to intermediate 3
and catalyses its conversion to intermediate 4.
A cyclic pathway is made up of many intermediate steps
that eventually result in an intermediate that is necessary
to keep the cycle moving.

The difference from the chain pathway is the regeneration of the intermediate, in this case
intermediate 4.
e.g. Krebs cycle and Calvin cycle.

Enzymes lower the activation energy of the

reactions they catalyse. Enzymes have active
sites on which the substrates fall on. The
activation energy is needed for the substrate and
the enzyme to collide. This results in the lock and
key mechanism. Also the activation energy can be
used to change or restructure the active site of
broad spectrum enzymes.

Enzyme inhibitors
Inhibitors are substances that reduce the rate of
an enzyme catalysed reaction. The inhibition may
be competitive. The inhibition can be caused by
an inhibitor actin on the active site of the enzyme
(competitive inhibition) or on another
region of the enzyme molecule (non-competitive
inhibition).
Competitive Inhibition
The substrate and inhibitor are chemically very
similar in molecular shape. The inhibitor can bind
to the active site. Enzyme inhibitor complexing
blocks substrates from entering the active site.
This blockage reduces the rate of the reaction.
However, if the substrate concentration is
increased it occupies more active sites than the
competitive inhibitor. Therefore the substrate out-
competes the inhibitor for the active site. The rate
of reaction will increase again.

Example: Succinate is converted to Fumerate by

Succinate dehydrogenase(SDase)
SDase can be inhibited by a later intermediate in the cycle
called malonate.
The presence of a competitive inhibitor decreases the rate
of reaction. Increasing the concentration of the succinate
reduces the effect of the inhibitor. At high concentrations
the succinate out-competes the inhibitory molecules for
the active site. The rate of reaction therefore increases.

Non-competitive Inhibition
The substrate and the inhibitor are chemically
different in molecular structure. The inhibitor
cannot bind to the active site as it has a different
shape. The inhibitor can bind to another region
of the enzyme molecule called allosteric site.
The bonding of the inhibitor with the enzyme
causes structural changes in the enzyme
molecule. The active site changes shape. The
substrate cannot bind to the active site and
therefore the rate of reaction reduces.

Example: Inhibition by metal ions (Ag+)

Silver ions inhibiting the formation of sulphide
bridges at the amino acid cysteine.
This changes the protein bonding and in turn the active site changes
excluding the substrate
The presence of a non-competitive inhibitor always significantly reduces the
rate of reaction.
When increasing the substrate concentration there wont be much change on
the rate of the reaction. However, you could increase the rate by adding more
enzymes.

Competitive Inhibitor Non-Competitive Inhibitor

molecule is similar to that of substrate molecule is different to that of substrate
the inhibitors block active site the inhibitors attach to the allosteric site which
then changes structure of the active site and
of the enzyme
inhibitor is similar ro substrate in chain inhibitor is not similar to substrate
structure
the reaction rate cab be increased by the reaction rate cannot be increased by
increasing substrate concentration increasing substrate concentration
Enzyme pathways can
be controlled by the
increased concentration
of the product from the end of the
pathway.
The principle is illustrated by the
transamination (change R group) of the
amino acid threonine to isoleucine.
Threonine is an amino acid that can be
converted to isoleucine by changing the
R group. This reaction is a chain
pathway. The substrate for the reaction is
Threonine. Isoleucine is the end product,
this molecule can inhibit the enzyme
threonine deaminase.
The inhibition occurs at an inhibition site
on the enzyme but not the active site.
An excess of end product (isoleucine)
switches off any more production of that
product, isoleucine.
At high concentrations, isoleucine
attaches to the inhibition site of threonine
aeminase. This attachment causes the
active site of the enzyme to change
blocking any further substrates.
Isoleucine, which is in high concentration
is used up in cellular processes that
require this particular amino acid.
The product concentration in the cell falls
and the isoleucine that is attached to the
enzyme threonine deaminase detaches
and the reaction resumes.

With the inhibitor removed the active site

becomes active again and the pathway
switches back on.

The product is again in production but

once high concentrations are reached
the pathways are once more shut down.
The process then cycles on in alternating
stages of production and inhibition. This
inhibition is similar to non competitive
inhibition. Allosteric enzymes are those
which have many binding sites. One is
the active site to which the substrate
binds so that the reaction can take place.
The other site (allosteric site) is where
another molecule (not the substrate) can
bind and change the shape of the active
site thereby inhibiting enzyme action.
Scientists use databases to identify potential new antimalarial drugs
Bioinformatics is an approach whereby multiple research groups can add information to a
database all others can view as well. One technique of Bioinformatics is Chemogenomics
which researches what metabolic pathways are present in an organism/virus/fungi with the aim
to find out if there is an inhibitor or not. If there is one, scientists will be able to kill the virus etc.
When a chemical binds to a target site (allosteric/active site), it can significantly alter metabolic
activity. Information on a large variety of chemicals is present in different organisms is available
as databases. Scientists developing new drugs can potentially use this information to test them
on one or many related organisms with particular metabolic pathways.

CELLULAR RESPIRATION
Cellular Respiration is a controlled release of energy from organic compounds in cells to form ATP.

C6H12O6 + O2 —> 6H2O + 6CO2 + ATP Cellular Respiration is the reverse of photosynthesis

The purpose of CR is to keep the body warm and metabolism going for us to do functions. CR
releases the energy from the food that we eat.

Plants also have to go CR even though they trap light energy. To store the energy for the purpose
of referring to this stored energy when they cannot undergo photosynthesis, they have to convert it
for all their metabolic activities to function as they require ATP as well to chemical potential energy.

ATP production ATP - Adenosine Tri Phosphate - is made and used

as required out of biomass. When the glucose
formed out of food and oxygen is broken, ADP is
released which reacts with Pi, an inorganic
phosphate, forming ATP.

Only the activities in the cell require ATP and no

other kind of energy e.g. active transport, producing
RNA/DNA, cyclists (movement of substances within the cell) etc.

When ATP is used up and is turned back to ADP + Pi + Energy, the rest of the energy is used up to
heat the body.
 Aerobic Respiration Anaerobic Respiration

Oxygen needed yes no

Products formed water, carbon dioxide, ATP ethanol, carbon dioxide, ATP

Level or breakdown of glucose All energy that is locked in

glucose is released

Number of ATP formed 38 ATP 2 ATP

Equation C6H12O6 + 02 —> 6H20 + 6CO2 C6H12O6 —> 2C2H5OH + 2CO2

+ 39ATP + 2ATP

Examples/Applications • making alcohol and bread

• animals can run longer and
faster a certain distance even
when the oxygen reaching the
muscles is low

Oxidation Reduction

electrons are removed é- electrons are gained é+

oxygen is added +O oxygen is removed -O

hydrogen is lost -H hydrogen is gained +H

The role of electron carriers and coenzymes in cellular respiration is very important. During redox
reactions the acceptor gets reduced and the diner gets oxidised at the same time. Co-enzymes
help enzymes to function during this reaction.

e.g. electron carrier carries hydrogen.

H+ + NAD+ +2é —> NADH + H+

This reaction is reversible because co-enzymes that carry Hydrogen take it to a place where they
have to release it again. They have to carry it because it is needed somewhere else.

Stage Location Needs O2 or not Reactants Products

Glycolysis cytoplasm no glucose pyruvate

(1 molecule) (2 molecules)

Krebs Cycle matrix of no

mitochondria

Oxidative cristae of yes

Phosphorylation mitochondria

All organisms perform glycolysis. The step proceeding glycolysis will depend on whether aerobic or
anaerobic respiration takes place. In yeast and plants living in water logged conditions, pirate
formed during glycolysis is converted to ethanol and CO2. In animals and humans, pyruvate can
be converted to latte during periods of strenuous muscle activity and anaerobic conditions. In
aerobic organisms, glycolysis is followed by the link reaction, Krebs cycle and finally oxidative
phosphorylation.
{Glycolysis, Link Reaction, Krebs Cycle, Oxidative Phosphorylation, Mitochondrion by hand}
PHOTOSYNTHESIS
 STAGES OF PHOTOSYNTHESIS

Phases Light Dependent Light Independent

Dependence of light Dependent Independent

Location in the chloroplast Granum because it contains Stroma because it contains

chlorophyll enzymes

Reactants H2O CO2

Products oxygen Glucose

Light dependent reaction

Cellular Respiration Combustion (burning)

Similarities release of energy, catabolic

use oxygen

release CO2 and H2O

substrate is organic

Differences energy released as ATP energy released through

light and heat energy

controlled energy release uncontrolled energy release

energy use is beneficial a lot of energy is wasted

Photosynthesis occurs inside chloroplasts, which contain chlorophyll that are found inside the
thylakoid membranes. The chlorophyll molecules are arranged in groups called photosystems of
which there are two types, Photosystem II and Photosystem I. The light-dependent reactions starts
within Photosystem II. When a chlorophyll molecule absorbs light, the energy from this light provides
the electrons inside the chlorophyll with energy. The chlorophyll molecule is then said to be
photoactivated. The electrons supplied with energy in the photosystem are then passed on from one
chlorophyll molecule to the next until it reaches the chlorophyll molecule at the reaction centre of the
Photosystem II that passes on the electron to a chain of electron carriers. This chain of electron
carriers is found within the thylakoid membrane. As the electron passes from one carrier to the next it
releases energy. The energy is used to pump hydrogen ions across the thylakoid membrane and into
the space within the thylakoids. This forms a concentration gradient, which allows the hydrogen ions
to travel across the membrane, down the concentration gradient. As the ATP synthase is located in
the thylakoid membrane, the hydrogen ions travel through it as they move across the membrane. It
uses the energy released from the movement of the hydrogen ions down their concentration gradient
to synthesise ATP from ADP and inorganic phosphate. The synthesis of ATP in this manner is called
non-cyclic photophosphorylation, because the hydrogen ions do not return to the inside of the
thylakoid.
The electrons from the chain of electron carriers are then accepted by Photosystem I. These
electrons replace electrons previously lost from Photosystem I. Photosystem I then absorbs light and
becomes photoactivated. The electrons are provided with energy again and then pass along a short
chain of electron carriers and are eventually used to reduce NADP+ in the stroma. NADP+ accepts
two electrons from the chain of carriers and one H+ ion from the stroma to form NADPH.
NADP+ is needed for the normal flow of electrons in the thylakoid membranes as it is the final
electron acceptor. However, there is often a shortage of NADP+. If NADP+ is not available then the
normal flow of electrons is inhibited. But there is an alternative pathway for ATP production called
cyclic photophosphorylation. It begins with Photosystem I absorbing light and becoming
photoactivated. The electrons from Photosystem I are then passed on to a chain of electron carriers
between Photosystem I and II. The electrons travel along the chain back to Photosystem I and as
they do so they cause the pumping of hydrogen ions across the thylakoid membrane and therefore
create a concentration gradient. As explained previously, the protons move back across the thylakoid
membrane through ATP synthase and as they do so, ATP is produced. Therefore, ATP can be
produced even when there is a shortage of NADP+.
The light dependent reaction not only produces NADPH as a waste product but also oxygen. When
the chlorophyll molecule at the reaction centre passes on the electrons to the chain of electron
carriers, it becomes positively charged. With the aid of an enzyme at the reaction centre, water
molecules within the thylakoid space are split and Oxygen and H+ ions are formed. The electrons
from the splitting of these water molecules are given to chlorophyll and the oxygen is excreted as a
waste product. This splitting of water molecules is called photolysis as it only occurs in the presence
of light.
Carbon fixation
Light independent reaction
The light-independent reaction of photosynthesis
takes place in the stroma of the chloroplast and
involves the conversion of carbon dioxide and other
compounds into glucose. The light-independent
reaction can be split up into three stages: the !
carbon fixation, the reduction reaction and
the regeneration of ribulose biphosphate. Together these stages are known as the Calvin Cycle.
During carbon fixation the carbon dioxide, that entered
the chloroplast by diffusion, in the stroma reacts with a
Reduction
pentose (five-carbon sugar) called ribulose biphosphate
(RuBP) to form a six-carbon compound. This
reaction is catalysed by an enzyme called ribulose !
biphosphate carboxylase, otherwise known as
rubisco. As soon as the six-carbon compound is
formed, it splits to form two molecules of glycerate
triphosphate. Glycerate triphosphate is then used
in the reduction reaction.
Glycerate triphosphate is reduced during the reduction Fate of trios phosphate
reactions to trios phosphate (three-carbon sugar). ATP
and NADPH + H+, that were both produced during
light-dependent reaction, provide the energy and
hydrogen needed for the reduction. Two trios
phosphate molecules can then react together to form
glucose phosphate. The condensation of many
molecules of glucose phosphate forms starch in the
form of carbohydrates stored in plants. However, out of
six trios phosphates produced during the reduction
reactions, only one will be used to synthesise glucose
phosphate. The five remaining trios phosphates will be
used to regenerate RuBP, which is essential for carbon
fixation to continue. Five trios phosphate molecules will
undergo a series of reactions requiring energy from
ATP, to form three molecules of RuBP. RuBP is
therefore consumed and produced during the light-
independent reactions and therefore these reactions
form a cycle that is named the Calvin cycle. !
DIGESTION AND ABSORPTION
NUTRITION
Nutrition is the taking in digesting, absorbing, and making use of food by the body.
There are different types of nutrition:
autotrophic - makes own food
heterotrophic - depends on somebody/something to get food
holozoic - food taken in through mouth and digested within body
saprotrophic - digesting food outside of the body and the taking in what is needed (only micro
organisms)

Organisms gain energy and matter from food. Energy is used for metabolism and matter is used
to build up the body.
Ingestion Taking in food intoto the body
Steps in nutrition Digestion Breaking down food physically and using
enzymes - Digestion is important to break
down big chunks to small pieces
(mechanical digestion) and to secret
chemicals (chemical digestion)

Absorbtion Digested food moving into the blood and

lymph from the alimentary canal

Assimilation Food becoming part of the body or being

used for metabolism

Egestion/Defaecation Getting rid of undigested food from the body

Excretion e.g. Urinating Getting rid of chemical waste from the body
Part Structural Adaption Enzymes Produced Main Function

Mouth • salivary glands • salivary amylase • Produced saliva

• teeth • mastication (chewing)
• tongue • swallowing
• taste food (wet food
tastes better than dry
food because water in
food breaks down
chemicals which the taste
pores are sensitive to)

Esophagus • longitudinal and • no digestion because • pushes food down with

circular muscles heart and lungs are longitudinal circular
there muscles

Stomach • gastric juice (for • pepsin (breaks down • mechanical digestion,

mechanical digestion) protein) chemical digestion and
• hydrochloric acid (acts • renin (breaks down low pH for killing
at low pH {about 2} milk) bacteria
killing bacteria) • lipase • Absorbs water (when
we have thirst there is not
enough water in the
blood. The concentration
of whatever changed
thickness and therefore
the volume of the blood to
reduce. The water goes
from the stomach directly
to the blood as the
molecules are small
enough)

Small Intestine • very long • Trypsin (digests • digestion of all the

• has villi and micro villi protein) different foods
(finger like structures • Amylase (digests
inside) that increase starch)
SA • Lipase (digests starch)
• muscles for peristalsis

Large Intestine • wider and shorter than • Symbiotic relationship

small intestine for with Vitamin K that
undigested food makes bacteria that
decomposes food

Rectum • short no enzymes • stores undigested food

• wide
Anus • sphincter (tube/ring of • controls the release
muscles that keeps
opening and closing=
Pancreas • feather shaped • Trypsin/Protease • Produces hormones
• Islets of Langerhans • Amylase (endocrine gland)
• exocrine cells in- • Lipase • Produces pancreatic
between patches that juice (exocrine gland)
produce pancreatic
juice
• two types of cells:
1. beta cells:
insuline
2. alpha cells:
glucagen

Common Bile Duct carries bilet pari juice

from Gallbladder to
Stomach

Liver • very big • produces bile (for

• cells are called digestion)
hepatocyte (they • detoxifies blood and
produce bile) body from
• alcohol
• smoke —> nicotine
• drugs
• medicine
• metabolises surplus
nutrients and stores
nutrients

Gall Bladder • sack that can store no enzymes • stores bile

(e.g. bile-when Gall • regulates its release
Bladder doesn't exist
anymore because of
gallstone for example,
then the bye is released
all the time)
• embedded/covered by
liver
Muscle layers of the small intestine

!
!

!
Lumen food goes through here

Crypts contains extensions of

interlining called vili and
micro villi to extend SA

Sub-Mucosa Between circular

muscles and villi

Circular muscles Many layers

Longitudinal muscles Many layers

Serosa slimey/soft
Prevents organ from
falling down whiles
running etc.
Peristalsis is the rhythmic contraction and election
of the longitudinal and circular muscles of the Mesentery Attaches intestines to
alimentary canal, which results in the moving forward wall of the body
or anything in the body that has to go through a tube.
When the food moves forward, through the alimentary canal, the circular muscles behind the food
contract making the tube narrow, This pushes the food forward. The longitudinal muscles inferno of
the bolus (food) contract making the tube wide. The circular muscles will relax. This contraction
and relaxation is repeated down the tube resulting in the food moving forward.

Importance of the pancreas in nutrition

Hormonal Function
Hormone Produced by When Produced Effect

Insuline beta cells of Islet of When blood sugar decreases blood

Langerhans level is high sugar level

Glucagon Alpha cells of Islets of when blood sugar raises blood sugar
Langerhans level is low level

Digestive Function
The pancreas produces pancreatic juice that is released into the lumen of the small intestine.
Enzymes in pancreatic juice

Enzyme Substrate acted on Products Formed

Amylase starch maltose

Lipase lipids fatty acid and glycerol

Protease protein and polypeptides peptones (short chain of fatty

acid)

Importance of the small intestine in nutrition

The wall of the small intestine has intestinal glands that produce and secrete enzymes into the
lumen of the small intestine. In addition, there are enzymes that are immobilised on the plasma
membrane of the epithelial cells of the small intestine. They are active in digesting the food in the
lumen of the small intestine. Theses cells may fall of and continue digesting food in the lumen of
the intestine.

Enzymes in the small intestine

Nuclease substrate: DNA/RNA produces nucleotides

Maltase substrate: maltose produces glucose

Lactase substrate: lactose produces galactose + glucose

Sucrease substrate: sucrose produces fructose + glucose

Exopeptidase substrate: peptone produces amino acid

Dipeptidase substrate: dipeptides produces amino acid

Cellulose is the nutrient that is not digested by humans as we don't produce cellulase. However,
this non digestion is important to humans as it promotes peristalsis.

Viili

The small intestine is adapted to increase the surface area for absorption by :
• being a long tube with many folds and projections
• having villi present of the folds
• having micro villi present of the villas

!
Epithelium cells • long and narrow
• contain extensions
called micro villi to
extend SA
• microvilli have
many mitochondria
undergoing active
transport

Lacteal • a branch of the

lymphatic system
• conducts fats away
from the villas after
they have been
absorbed

Lymph Vessel • (horizontal) branch

where lacteal flows
into again

Capillaries Connections between Absorption of digested food in the small intestine

Arteriole and Venule

Arteriole and venule Arteriole - small

branch of artery that Nutrient Enzymes Digested
brings blood in Products
Venial - small vein
Carbohydrate Amylase Maltose
that takes blood out

Triglyceride Lipase Glycerol

(lipid) Fatty Acids
Longitudinal
Muscles and Phospholipid Phospholipase Phosphate
Circular Muscles Glycerol
Fatty Acids
Serosa underneath muscles’
Proteins Protease Peptones

Nucleic acids Nuclease Nucleotides

Mineral ions
no enzymes or products because
they are in their simplest for already
Vitamins

Methods of membrane transport required for absorption of nutrients in the small intestine

The mechanism involved in the absorption of digested food are simple diffusion, facilitated
diffusion, active transport and endocytosis.
! Absorption of triglycerides

Triglycerides are hard to digest because they are

insoluble in water. They move through the
endoplasmic reticulum to the Golgi apparatus and
are then released within vesicles.

Absorption of Fatty acids

Short Chain Fatty acids • The fatty acids are pushed in by the bile
salts
• Enter the cell through diffusion • Once its inside it doesn't need the bile salts
• are absorbed by the blood capillaries as it binds with glycerol again and forms a
triglyceride
Long Chain Fatty acids • The triglyceride is covered by a protein and
forms a chylomicron
• Fatty acids and glycerol are products of lipid • This is taken in by a vesicle and transported
digestion out of the cell through exocytosis
• Absorbed by simple diffusion • The chylomicron is absorbed by the vessels
• Some FA are absorbed by facilitated immediately
diffusion
Absorption of glucose

• Glucose is polar and hydrophilic

• Cannot pass by simple diffusion
• Sodium potassium pump on the epithelial plasma membrane
• Pumps sodium out of the epithelial cell
• Reduces concentration of sodium in the epithelial cell
• This causes sodium and glucose to passively move into epithelial membrane through facilitated
diffusion using a co-transport protein
• Glucose moves through facilitated diffusion into blood vessels

Starch digestion and absorption

• Salivary and pancreatic amylase are the
enzymes
• Can break the 1-4 bonds as long that there
are a min. 4 glucose monomers on the chain
• Amylose is hydrolysed into maltose (2
monomers) and maltotriose (3 monomers)
• Amylopectin is hydrolysed into above 3 and a
fragment containing the 1-6 bond called
dextrin amylopectin
• Membrane bonds enzymes named maltose,
glucosidise and sextrinase breaks all the
fragments to glucose
• Glucose is absorbed by CO transport with
sodium ions
• Passes into blood capillaries who's
 endothelium havee pores to absorb glucose
• moved to being and carried to the liver

THE BLOOD SYSTEM

The blood system continuously transports substances to cells and simultaneously collects waste
products (e.g. CO2, Ammonia, Urea).
The circulatory system is made up of
the heart, the blood vessels, blood and
cardiac centre.
Heart - Pumps blood
Blood Vessels
Artery - comes from the heart; carries
oxygenated blood to the organs of the
body
Vein - comes from the organs; carries
deoxygenated blood to the heart
Capillary - tiny blood vessel that carries
look to the cells from the main artery
Blood - carries oxygen, nutrients,
waste, products, blood cells, heat.
Cardiac Centre - in the brain; controls
the heart rate.

The structure of the Heart

Blood Vessel Origin Takes blood Brings blood to…. Type of blood
from… carried

Aorta artery left ventricle all the organs of the oxygenated

biggest blood body
vessel

Pulmonary artery artery right ventricle lungs deoxygenated

Pulmonary/ vein lungs left atrium oxygenated

Semilunar vein

Inferior vena cava vein all organs below right atrium deoxygenated
the heart

Superior vena vein all organs above right atrium deoxygenated

cava the heart

Coronary artery artery aorta heart tissue oxygenated

Coronary vein vein heart tissue superior vena cava deoxygenated

Bronchial artery artery aorta lung tissue oxygenated

Bronchial vein vein lung tissue superior vena cava deoxygenated

Heptic artery artery aorta liver tissue oxygenated

Hepatic vein vein liver tissue inferior vena cava deoxygenated

Hepatic portal vein intestines, stomach liver tissue deoxygenated

vein pancreas

The cardiac cycle

The initiation and control of the heartbeat

• Whenever a message is brought through a nerve it is called

a nerve impulse.
• Those messages are send from the cardiac cycle to the SAN (Sino Atrial Node).
• The message tells the muscles to contract, the passes on to the area and so both area contract
• The impulse of the SAN is passed to the AVN (Atrioventricular Node - between atria and
ventricle)
• From the AVN down to the septum and then up the ventricular walls
• This results in ventricular systole

The heart rate is controlled by the nerve impulses reaching the heart via two nerves. These nerves
arise from the medulla oblongata of the brain. They re the accelerator nerve, which increases the
heart rate when stimulated, and the decelerator nerve, which decreases the heart rate when
stimulated. The heart rate is also affected by certain factors in the body which lead to the
stimulation of the two nerves. Accordingly, the heart rate may increase or decrease. Theses factors
are blood pressure, oxygen concentration, pH and certain hormones.
If blood pressure increases, the heart rate decreases
systolic pressure - low reading
diastolic pressure - high reading

If there is a lot of blood pressure, there is a lot of blood in the blood vessels and a lot of blood is
flowing in the body. By reducing the heart rate, you can control the blood flowing through the body.
Things that increase blood pressure like being nervous or stressed increase it because there is a
high heart rate.
e.g. When a person has an accident and has lost a lot of blood the heart rate is very fast. When
blood pressure is low, the heart rate is fast.

When the oxygen concentration in the blood is hight, the heart rate goes down. When the heart
rate is high, more oxygen has to be pumped to the muscles
e.g. after exercising, when you're resting/sleeping

If the pH is high, the book gets alkaline and if the pH is low, the blood gets acidic. If the pH is too
high, the heart rate decreases; if it is too low, it increases. The last factor that effects the heart rate
is epinephrine which is the hormone adrenaline. The body produces it in a fight or flight situation to
increase metabolism,. If it goes up, the heart rate goes up too.
Veins, Capillaries and Arteries
The circulation of blood
Causes and consequences of occlusion of the coronary arteries
• lipids
• low density lipids flow easier and are always present, they start sticking to the walls of the
arteries which then clump. Phagocytes and muscle cells interact, they form a covering over the
clumps which thickens the walls and makes them inelastic —>atherosclerosis. At the latest
stage, the artery can rapture. It creates tension leading to clotting of blood. When a cloth is
formed, it is called thrombosis. This can happen anywhere throughout the body because high
blood sugar, high blood pressure, transfers etc. If there is coronary thrombosis the heart
muscle doesn't get enough nutrients and oxygen so they start quivering contracting and
relaxing very quickly without rhythm which can lead to a heart attack.
• High density lipids becomes fat that is stored because it is to sluggish for carrying

ECOLOGY
{SEPERATE WORKSHEETS}