Chapter 2 CELLULAR ACTIVITY

All organisms are made up of cells

The Cell Membrane
Plasma Membrane
Physical Barrier: Separates contents of cell (intacellular fluid from
extracellular environment)
Regulates what goes in and what comes out
Communicates with neighbouring cells (receptor proteins)
Sensitivity: Detects changes in the extracellular fluid e.g. drop in blood sugar
Support: Gives cell shape

Structure of Cell Membrane

Phospholipid bilayer
Fluid mosaic model
- Fluid: the molecules are constantly moving
- Mosaic: there are many different types of molecules
Lipid molecules containing a phosphate group
Hydrophilic (water loving) head
Hydrophobic (water hating) tail
Cholesterol is embedded between the phospholipids

Proteins are embedded in the bilayer

- Channel proteins pass through the entire membrane and have a central pore
to allow ions, water and other small molecules to pass through
- Carrier proteins extend the length of one layer and carry substances across
the membrane

Membrane Proteins
Receptor Proteins
Channel proteins
Carrier Proteins
Cell-Identity markers
Membrane Transport
Diffusion
Diffusion is the movement of molecules so that they are evenly spread over
available space.
Cell membranes are differentially or semi-permeable which means only some
substances can pass through easily while others are unable to get through
without help or at all.
An ion or a molecule can diffuse through a cell membrane two ways;
- Substances soluble in lipids (eg alcohol, steroids and fatty acids) as well as
carbon dioxide and oxygen, can diffuse through the lipid part of the membrane
- Substances can pass through membrane channels formed by channel
proteins. Small water soluble molecules (e.g. sodium and calcium) can fit
through the membrane (only if they are small enough).
Osmosis is the diffusion of water through a semi permeable membrane from
an area of high water concentration to an area of low water concentration. It is
a passive process.

Carrier Mediated Transport

Molecules bind to proteins in the cell membrane to be transported across the
membrane.
Carrier proteins are specific they will only bind to certain molecules
Carrier proteins can become saturated they can only bind to a certain number
of proteins (saturation point)
Transport is regulated by hormones
Two types: Facilitated Diffusion and Active Transport
- facilitated diffusion is a passive process. It is the movement of molecules
from a high concentration to a low concentration by binding to a carrier
protein. The molecule attaches to the binding site on the protein, the carrier
changes shape and releases the molecule on the other side of the membrane.
- active diffusion is the transport of molecules from a low concentration to a
high concentration. It is an active process and uses ATP molecules. Molecules
travel across the membrane similar to those in facilitated diffusion, only going
against the concentration gradient.
Vesicular Transport
The movement of substances across the cell membrane is membranous bags
called vesicles. Is an active process.
Endocytosis: Bringing substances into the cell. The cell membrane folds
around a droplet of liquid or a solid particle until the droplet or particle is
completely enclosed. The vesicle then pinches off and enters the cytoplasm.
- Pinocytosis: Cell drinking
- Phagocytosis: Cell eating
Exocytosis: Substances exiting the cell. Vesicle containing substances
migrates to the cell membrane and fuses with the membrane. The vesicle then
opens and the contents are pushed out.
TYPE OF TRANSPORT
DIFFUSION

PASSIVE/ACTIVE
Passive

Osmosis
CARRIER MEDIATED
Facilitated Diffusion
Active Transport
VESICULAR TRANSPORT
Endocytosis

Passive

Passive
Active

Active

Exocytosis

Active

SUBSTANCES
Water, O2, CO2, alcohol, fatty
acids, steroids, ions (Na, K, Ca),
lipid soluble drugs.
Water
.
Glucose Amino Acids
Certain ions (glucose, AAs)
.
Cholesterol, iron ions, microorganisms and cell debris but
only by certain specialized cells
Secretions like mucus or
digestive juices

Membrane Receptors
Some proteins in the cell membrane are receptor proteins

Bind with certain molecules outside the cell and trigger a response/reaction
within the cell
Specific each type of receptor will bind with one type of molecule (lock and
key analogy)
Different cells have different types and numbers of receptor proteins therefore
there is a variation in the sensitivities of cells to hormones and other
substances
Receptor proteins also help in the communication with other cells

DNA
A DNA molecule is made up of thousands of nucleotides
Each nucleotide consists of ribose (a 5-carbon sugar), a phosphate group and a
nitrogenous base

Phosphate Group
Ribose (deoxyribo (one less oxygen) in
DNA and ribo.. (normal) in RNA-full oxygen
compliment)

Nitrogenous Base (adenine +

thymine (uracil in RNA), cytosine + guanine)
OH
Hydroxyl
Group

H
Hydrogen

The two chains of alternating sugars and phosphates are known as the sugarphosphate backbone
The bases (once joined) can be seen as the rungs on a ladder
The two strands twisted together are known as a double helix
A chromosome contains approximately 140 million base pairs

Functions of Proteins
Structure: Strengthening hair, nails, skin (keratin) and strengthening and
making bone, cartilage, deep skin layers flexible (collagen)
Transport across membranes: carriers and channels.
Communication: Hormones, receptors
Cell metabolism: enzymes determining chemical reactions
Recognition: Immune system wont attack own cells but foreign proteins will
stimulate the production of antibodies
Movement: Can change shape and move structures within the cell or can move
whole cell (eg muscle c
Chapter 3 CELL PROTEIN PRODUCTION

mRNA: an RNA molecule that carries genetic information from the DNA in
the nucleus to the ribosomes

tRNA: a small RNA molecule that carries an AA to the ribosome and places it
in the correct position determined by its corresponding mRNA
Gene: part of a DNA molecule that contains all the triplets needed to produce a
specific protein
DNA: a molecule in the nucleus of a cell that determines the types of protein
that a cell can make. Holds the genetic information
Chromosome: rod-like structures in the cells nucleus that carry the hereditary
information
Triplet: a section of DNA 3 bases long
Codon: a section of mRNA 3 bases long, codes for a particular AA

Protein Synthesis
Translation

The mRNA strand undergoes modification before it leaves the nucleus. The introns
(non-coding sections) are removed from the strand, leaving only the exons (coding
sections).
Translation
Translation is the production of the protein that is coded in the mRNA strand. The
mRNA travels into the cytoplasm and a ribosome attaches to one end of the strand
(where the binding site of bases are ensures ribosome attaches to correct end of
mRNA).

The ribosome then moves along the strand of mRNA, reading it 3 bases (a codon) at a
time. It appears as though the ribosome is pulling the strand through itself like a
ribbon.
The codon AUG (methionine) is the start codon. It is different to the binding site
bases. When the ribosome reads this codon it can begin coding the mRNA strand and
producing the protein. Therefore ever proteins amino acid sequence originally begins
with methionine (it can be removed later if not required for the function of the
protein).

As each codon is read,

the tRNA with the
matching anticodon,
binds to its
corresponding amino
acid and brings it down
to the mRNA strand.
Here it binds to its
corresponding mRNA
codon. The amino acid
forms a peptide bond
with the amino acid next
to it (using one ATP
molecule) and the tRNA
breaks off and goes back
into the cytoplasm
leaving behind the AA.

Summary of Protein Synthesis:

Transcription:
- Two strands of the DNA in a gene separate coding and template
strand
- mRNA forms complementary to the bases on the template strand
- modification: introns are removed to leave only exons
- mRNA travels to the cytoplasm
Translation:
- mRNA attaches to ribosome
- ribosome moves along strand reading codons until it reached AUG
(start codon) when it will begin coding the mRNA and making the
protein
- for each codon, a tRNA molecule with matching anticodon brings the
correct AA
- AAs are bonded together to form peptide chain (1 ATP molecule per
bond) which is the protein
Protein Structure
Primary (1) Structure: A chain of AAs joined by
peptide bonds. The sequence of AAs that make up
the protein. A protein may have 10 000 or more
AAs in the chain and changing just one of these can
significantly change the proteins properties and in
turn, the function of the body.

Secondary (2) Structure: Is either a coiled or folded

shape. Is made by bonds between different parts of
the AA chain. Forms sheets or spirals.

Tertiary (3) Structure: Is formed by further bending

and folding of the protein into globular or fibrous
shapes.

Quaternary (4) Shape: (Some proteins) Is formed

when two or more AA chains interact/join.

Modifying and Packaging of Proteins

AA chain goes to the Golgi Apparatus (or Golgi Body) where SUGARS,
PHOSPHATES, sulfates, fatty acids and other molecules (depending on the
desired protein) are added to create a functional protein
- DNA holds info to make proteins, which make enzymes, which make
carbohydrates and lipids. Therefore, DNA is indirectly responsible for the
synthesis of lipids and carbs.
Chapter 21 BIOTECHNOLOGY
HUMAN GENOME PROJECT
The human genome project is an international research effort aimed at
mapping the entire human genome. It commenced in 1990 and was completed
in 2003 though there is still much research to do
So far, around 4000 genetic disorders are known
The HGP has identified the location of all of these potentially faulty genes and
replacement of these genes has become a possibility
Information gained from HGP has also influenced many other lines of
research: new technology is being developed to monitor the expression of
genes involved in particular diseases (e.g. colon cancer) and genetic tests have
been improved to inform individuals if they are high risk for a particular
disease.
DNA
A genome is the complete set of genetic information of an organism.
There are approximately 20 000 25 000 genes in our genome.
It is important we know the Human Genome to;
- discover genetic disorders
- allow for replacement therapies and
- to understand gene expression
Biotechnology has allowed us to identify hereditary diseases and mutations
DNA Profiling
Everyones DNA is unique (save identical twins)
Can be used to identify an individuals identity or parentage (e.g. remains at a
crime scene)
Can also be used in anthropological research detecting genetic variation
and/or mutations that may play a role in the development of a disease
A DNA profile can be created from the smallest/oldest and most damaged of
DNA samples.
From this tiny sample of DNA, many copies are made through the process of
polymerase chain reaction (PCR)
DNA Sequencing

Is the determination of the precise order of the nucleotides in a sample of

DNA
The method most commonly used to determine this sequence was invented by
FREDERICK SANGER
Our nucleotides (Deoxynucleotide Triphosphates) are bonded together via
their hydroxyl groups

OH

OH

OH

OH

Without the Hydroxyl group, the nucleotides

cant bond together.
Therefore, artificially made nucleotides,
have another Hydrogen where the Hydroxyl
group should be.
This means that this artificial nucleotide
cant join to another nucleotide, hence
stopping the DNA molecule from growing
and lengthening.

The sequence that has been shortened is then more easily compared to the
DNA sequences in question
It is also a lot easier working with smaller, more manageable sections of DNA

DNA Sequencing Process

The DNA is separated into two strand (by heating)
The strand to be sequenced is copied using synthetically altered bases
(thousands and thousands of copies)

These altered bases cause the

copying process to stop each
time one particular letter (e.g.
G guanine) is incorporated
into the growing DNA chain

The location of that particular

base can then be located on
the strand of DNA

This process is carried out for

all four bases, and the
fragments are put together like
a jigsaw to reveal the
sequence of the original piece
of DNA.

By comparing DNA sequences, changed alleles and mutations can be

identified and will show whether an individual has a particular disease.

Electrophoresis

DNS strands can be chopped up into smaller fragments using special enzymes
and sorted according to their size

Gel Electrophoresis
The samples to be tested are injected into small wells in a sheet of porous,
jelly-like material
An electrical current is then passed through the gel and the fragments are
drawn towards the positive end
The small fragments travel faster (and therefore faster) than the larger ones

DNA profiling can be used for detecting genetic variations and/or mutations
that may play a role in the development or progression of a disease.

Polymerase Chain Reaction (PCR)

Is like a biological photocopier.
Is used for creating multiple (thousands) of copies of a specific segment from
a DNA sample (DNA amplification)
Is useful when only small amounts of DNA are available for analysis
PCR contains many steps
Initialising: (94 96C)
- used if the DNA polymerase requires a heat activation
Denaturation: (96 98C)
- thermal cycling: repeated heating and cooling of the DNA (aka DNA
melting)
- disrupts hydrogen bonds located between the base pairs resulting in two
single strands instead of a double helix (strand unzips)
Annealing: (50 65C)
- primers attach to the templates
- DNA polymerase binds primers to the template strand and begins synthesis
Elongation/Extension: (temp dependent on DNA polymerase used)
- if TAQ (thermos aquaticus bacteria) polymerase is used 75 80C
- DNA polymerase synthesizes a DNA strand
- the time it takes depends on the polymerase used and the length of the strand
- optimum speed/level: 1000 bases/min

These 3 steps are repeated as necessary (before final step)

Final Elongation: (70 74C)
- after the last PCR cycle
- this ensures any remaining strands are elongated
runs for 15 minutes
Final hold: (4 15C)
- allows for stoppage and storage of the reaction

Recombinant DNA Technologies (aka Genetic Engineering)

Involves the
introduction of DNA
from one organism
into the DNA of
another organism.
Has the huge potential
of replacing faulty
genes with healthy
ones
Can help patients
suffering from cystic
fibrosis, rheumatoid
arthritis and certain
cancers
Transgenic organisms
are those whose

genome has been altered by the transfer of a gene or genes from another
organism
These transferred genes become part of the organisms DNA and therefore can
be passed on to the next generation
Recognition site: a point where there is a specific sequence of bases where
restriction enzymes cut
Recombinant DNA technologies (RDT) have had a huge impact on the
diagnosis and treatment of diseases and genetic disorders
Using RDT the human gene that has the code for insulin production was
introduced into bacterial cells. These bacteria became insulin factories and are
now cultured in vats where they produce insulin that can be used to treat
diabetes. This procedure is now frequently used with yeast cells instead of
bacterial cells.
The production of vaccines using recombinant DNA technology is very
expensive and there is often no incentive to make a vaccine as it is paramount
they are safe due to the large population (mostly children) they are used on.

Gene therapy
Used to treat or cure genetic abnormalities by replacing faulty genes with
healthy ones. Uses the genes themselves as treatment.
Unlike most conventional medicines, gene therapy has the potential to actually
cure the disease as it is replacing the faulty gene.
Gene therapy is being used to find a cure for Cystic Fibrosis. Because it is a
singe gene disorder and it mainly affects the lungs, which are relatively easy to
access and provide treatment, it is a logical choice for gene therapy treatment.
The first trial was in 1993. Researchers modified a common cold virus to act
as a vector and carry the normal genes to the Cystic fibrosis transmembrane
regulator cells in the airways of the lungs. Since then, researchers have studied
and tested other modes of transport for the normal genes; fat capsules, nose
drops, synthetic vectors etc.
Gene therapy is also being used to treat huntingtons disease. Huntingtons
Disease is caused by a mutation on a single gene which produces a mutated
form of the enzyme Huntingtin, which results in nerve cells in he brain being
damaged causing physical, emotional and mental changes. Researchers have
experimented on mice and using gene therapy have been able to shut off or
silence the gene that codes for the huntingtin protein. However this can not be
tested on humans as the brain cells may not be able to survive without the
huntingtin protein.
Genetic Probe
A fragment of DNA (or RNA) labeled with radioactive isotopes or a
fluorescent marker used to detect the presence of a specific sequence of bases
in another molecule
The DNA section that is being inspected is denatured and split into two strands
The genetic probe is then incorporated into the DNA and binds to it (the
original section of DNA is replaced by the probe).
The end result is a highlighted gene or fragment of DNA on a chromosome.

This process is used extensively to detect Duchene muscular dystrophy and

Thalasseamia
If the gene in question is normal/healthy the genetic probe will bind to the
DNA and the gene will be highlighted. If the gene is abnormal, the genetic
probe wont be able to bind to the DNA and nothing will be highlighted
Many techniques are used to detect the presence of a mutant gene;
- DNA sequencing
- Profiling techniques
- Polymerase Chain Reaction (PCR)
- Genetic Probes
- Genetic Engineering (recombinant DNA technologies)

Chapter 14 INHERITANCE
Gene: Coding sections, for the factors that determine hereditary diseases, on
the chromosomes
Allele: Alternative forms of the same gene
Chromosome: Rod-shaped structures that carry the hereditary information
Loci/lucus: The location of a gene/ genes on a chromosome
Gene Linkage: Certain characteristics tend to be inherited as a set
Multiple Alleles
Still one gene, however there are more than 2 alleles and more than 2
phenotypes
E.g. Blood Types
ABO Blood Typing
As, Bs and O/s code for antigens that are present on the cell membrane of
RBCs
Antigen A = IA
Antigen A + B = IAIB
Antigen B = IB
No Antigen
= i
A
B
I and I are co-dominant blending of characteristics
i is recessive
Monogenic Inheritance
There are many alleles but the pattern of inheritance is one with discrete
characteristics
Each person has only one pair of alleles for the characteristics (e.g blood type)
Polygenic Inheritance
The inheritance of the characteristic is dependent on many genes, not just one
pair
The environment may also influence the expression of these characteristics
(e.g. diet, exercise, UV radiation, disease causing organisms)
Hair colour, weight, height and skin colour

Skin colour: People arent either black or white, they are all a variety of
shades. AABBCC codes for the darkest skin possible (Sudanese people) whilst
aabbcc codes for the whitest skin possible (Norwegians or Greenlanders)

Height: influenced by a number of factors (e.g. North Koreans vs South

Koreans North Koreans are shorter as they have an inadequate diet)
Effects of the Environment on Gene Expression
The skin colour of an individual depends mainly on the amount of melanin
they contain, a yellow-black pigment produced in special skin cells called
melanocytes.
Melanocytes produce structures called melanosomes which contain melanin.
In individuals of darker skin, the malanocytes are larger, contain moremelanin
and are more evenly distributed.
One of the biochemical processes occurring in melanocytes will produce large
amounts of melanin when stimulated by the ultraviolet rays from the sun.
Height is drastically affected by diet. A diet deficient in essential proteins and
minerals may result in a person not achieving their potential height.
Conversely, a person who has an excessive food intake may exceed their
expected weight when looking at their family background.
The deficiency of Iodine in the diet of pregnant women can lead to cretinism
in the child, retarded physical and mental development.
Gene Expression
The process of copying information from DNA onto mRNA and then
translating the message into a series of amino acids to form a protein (the
mechanics of gene expression are protein synthesis)
Transcription doesnt occur until the DNA polymerase locates the promoter
4 Sources of variation:
- Gene expression
- Environment
- Inheritance
- Epigenetics
Epigenetics
the factors that are inherited that make genes more or less likely to be
expressed
Epigenetic (beyond genetics): the altering of the expression of a gene without
changing its structure
Chapter 15 EVOLUTIONARY MECHANISMS
Population: a group of organisms of the same species living together in a
particular place at a particular time

Gene Pool: the collection of genotypes of all the individuals that are capable
of reproduction (not infants) in a particular population
Allele Frequencies: the occurrence of alleles of a gene in a population studied
Species: a group of individuals that share many characteristics and are able to
interbreed under natural conditions to produce fertile offspring
There are 4 ways to change the allele frequencies in a population:
- Mutations
- Natural Selection
- Random Genetic Drift
- Barriers to Gene Flow
Mutations
Random, non-inherited variations appearing with no precursor and purely by
chance
Mutant: an organism with a mutation
Gene mutation: change in a single gene so the traits normally produced by that
gene are changes or destroyed
Chromosomal mutation: all or part of a chromosome is destroyed
Somatic mutations: mutations occurring in somatic (body) cells that are not
passed on to the next generation
Germline Mutations: mutations that occur in the reproductive (germinal) cells
that are passed on to the next generation
Natural Selection
Charles Darwin: Father of Evolution. A naturalist who proposed and proved
with scientific evidence that all species of life have evolved over time from
common ancestors through the process of natural selection
Forms the basis of the modern evolutionary theory
Can be viewed as the selection of genes in a population that give an organism
a greater chance of survival. The organisms that survive can pass on their
genetic information (with these favourable characteristics) and gradually over
a long period of time, the population will become better suited to the
environment
Natural selection CANNOT occur in a changing environment
There are 3 observations that for the theory of Natural Selection:
- Variation: All members of a species vary and these variations are passed on
from generation to generation
- Birth rate: all living things increase their numbers at a rate greater than their
available resources allow (food, shelter, water etc)
- Natures Balance: although the birth rate of organisms was very high, the
species tended to maintain their numbers at a relatively constant level

There are 2 interpretation of natural selection

- Survival of the Fittest: Due to the struggle for existence organisms with the
characteristics better suited to their environment where more likely to survive,
reproduce and pass these favourable characteristics on to the next generation
- Struggle for Existence: Because of the high birth rate and limited resources
there was a struggle for existence, to survive

Examples of natural selection in modern humans:

- Sickle cell anaemia is abundant in Malaria prone areas as individuals with
the sickle cell anaemia trait (one recessive allele) are immune to malaria
- Skin Colour: Individuals who live around the equator have darker skin as to
absorb minimal Vitamin D as possible when in the sun and to give them a
better protection against UV rays whilst people who live around the poles have
lighter skin as to absorb as much vitamin D as possible during the minimal
times they see the sun.

Genetic Drift
In small populations there is often a random, non-directional variation in allele
frequencies. An allele that is rare in large populations may become frequent in
small populations. Occurs over a period of time
Also Known as the Sewall Wright effect
Only occurs in SMALL populations
Small populations are created due to isolation (socio-cultural and geographical
barriers) or when a small group moves away from the original population
Barriers to Gene Flow
Isolation: A barrier prevents interbreeding between populations thus, creating
separate gene pools
Environmental pressures change and will result in different characteristics
being selected, changing the allele frequencies of the two populations.
The changes in alleles frequencies change the characteristics of the
populations and results in subspecies or different races
Geographical barriers: Oceans, large lakes, mountains, deserts, extensive ice
sheets.

Socio-cultural barriers: Developed as human cultures became more complex.

Religion, economic status, education, social position (main 4) and language
(to some extent).

Gene Flow: The transfer of genetic information from one population to

another. If isolation has been extreme and over an extended period of time, it
may not be possible for populations to interbreed if they come together again
Speciation: The formation of new species. For a new species to form (e.g.
between two separated populations), there needs to be variation within both
populations, isolation of the two populations, environmental pressures
(weather, UV, diet, chemicals) and it needs to occur over an extended period
of time.
Founders Effect: Similar to Genetic Drift (except change is more immediate).
When a small population moves away from the original population and
establishes a new community. This new community is not genetically
representative of the homeland population and usually shows non-typical (for
the original population) characteristics.
E.g. the bounty mutineer descendents (with native Tahitian men and women)