DNA and the Genetic Code

Gene: a series of base sequences

Multiple genes code for a DNA strand.
A DNA strand wrapped up is known as a chromosome.

Human Genome Project

Began in 1990, unexpectedly finished 4 years earlier in 2001 due to

unanticipated technological advancements.
Determined the number of all human genes, their locations, and many of their
key base sequences. Genomes of other species have also been determined.
Genome full set of genes and alleles found in a species
Allowed geneticists to identify mutations and investigate the interaction
between different genes and the proteins they code for.
Made possible by the development of fast computers, international sharing of
data
DNA
DNA is deoxyribonucleic acid is found in all living cells. It is the genetic
blueprint of an organism.
The DNA molecules of all living things on the Earth have the same general
structure, but each species has its own unique DNA that defines the species.
There are also slight differences in the DNA between individuals within a
species, which is why we are all unique.
James Watson and Francis Crick worked together at the University of
Cambridge in the United Kingdom during the early 1950s. They discovered
the structure of DNA, but did not carry out any experiments.
The main advancement which led to Watson and Cricks discovery was carried
out by Rosalind Franklin. She carried out X-ray crystallography to obtain
pictures of DNA, this hinted that the structure of DNA is a double helix.
The four bases of DNA are: adenine (A), guanine (G), thymine (T) and
cytosine(C).
The structure of DNA is composed of multiple nucleotides, the basic unit of
nucleic acids. These are made up of 3 components:

A nitrogenous base(A,T,G,C)

A 5 carbon sugar
A

phosphate group

The sugar and

phosphate group form the
sides of the double helix
structure, the sugarphosphate backbone. The
bases are attached to
the sugars and form the
rungs of the double
helix ladder. Any number of
nucleotides can join
together, in any order, to form the nucleic
acid polymer, or
polynucleotide chain.
Watson and Crick
realised that the bases on one of the
polynucleotide chains are bonded to bases on the other polynucleotide chainA always bonding to T and G always bonding to C. These bases were called
complementary bases or complementary base pairs.
Two polynucleotide chains, or strands, are attracted to each other due to the
chemical nature of the complementary bases. This is important for the easy
unzipping of the ladder during replication. A large base (adenine or guanine)
is always bonded to a small base (thymine or cytosine) because this gives a
consistent amount of space between the strands.
RNA is a single-stranded polynucleotide with a similar sugarphosphate
backbone to that of DNA. However, RNA contains the sugar ribose and the
four bases adenine (A), guanine (G), cytosine (C) and uracil (U) instead of
thymine (T), it does not contain the phosphate group. RNA plays a key role in
protein synthesis.
The number of chromosomes per species is always an even number because
chromosomes exist in homologous pairs.
A gene is a length of DNA that has a specific sequence of base pairs and
codes for a particular characteristic.
A karyotype is an image of a chromosome extracted from a cell, stained and
photographed through a digital microscope. This is used to identify genetic
abnormalities.
The genes that make up chromosomes hold the code for every characteristic
of an organism. A full set of these blueprints is present in almost every cell of
a multicellular organism. The few exceptions include red blood cells, which do
not have a nucleus, and gametes (sperm and ova), which only have one set of
chromosomes rather than pairs.
Cell Division
There are 2 forms of cell division- mitosis and meiosis

Mitosis is an organised series of steps of a cell division that

ensures each daughter cell is an exact copy of the parent cell.
Chromosomes are inner parts of the cell which divide and replicate

themselves to create new cells.

Meiosis is a type of cell division where gametes are formed in the

ovaries or testes of an organism. Meiosis results in a daughter cell

Meiosis 1

Meiosis 2

receiving half of each parent cell.

Meiosis I separates homologous pairs of chromosomes
Meiosis II separates chromatids
DNA makes copies of itself through a process known as replication. In
replication

DNA unzips by breaking the hydrogen bonds between the

nitrogenous bases, with the help of enzymes and heat.

Spare nucleotides which are floating around in the nucleus are

added to the other side of the bases, which ensures that the DNA is
replicated fully.
Replication is the first stage of both mitosis and meiosis, and every
chromosome is replicated. After replication, the doubled chromosomes are
still attached at a point called the centromere and the chromosomes often
look like an X.
Chromosomes are commonly drawn like this because it is the stage at which
they are most easily visible under a microscope. Each strand of the doubled
chromosome is called a chromatid.
Key things to remember about replication:
Before replication: single chromosome = 1 molecule of DNA (doublestranded double helix) = 1 copy of every chromosome
After replication: doubled chromosome = 2 molecules of DNA = 2 chromatids
joined at the centromere = 2 copies of every chromosome

Mitosis is the process of replicating exact copies of somatic cells.

Meiosis is the process by
which diploid cells are
converted into haploid
gametes
and it occurs in the

gonads of
multicellular, sexually reproducing
organisms.
The only purpose
a gamete is to

of
fuse or join with another
gamete to make a new cell
called a zygote. This fusion
of
gametes is called fertilisation.
The
zygote will be diploid because it contains two sets of
chromosomes, one from each gamete. Therefore, the original number of
chromosomes is restored again in the body cells of the new organism
Mutations
Mutations are mistakes made during both replication and cell division. They
can involve individual genes or entire chromosomes.
A gene mutation is a change to the sequence of bases within a gene and
usually happens during replication. Generally mutations are fixed by
enzymes, specialised helper proteins that act as proof-readers. The impact of
these mutations varies depending on the nature of the change to the genetic
code.
Sometimes the mutation can cause the base to change, but the new codon
still codes for the same amino acid, so this is still fine for the body. Other
times the mutation changes the amino acid, and this starts a chain reaction,
affecting the protein and eventually the body.
Natural, spontaneous mutations occur continuously at a low rate. However,
environmental factors called mutagens can increase the frequency of
mutations. Mutagens include chemicals, radiation and ultraviolet (UV) light.
Somatic mutation- occurs during mitosis of body cells (diploid cells). The
effect of this mutation only occurs to the person with the affected cells.
Sometimes, somatic mutations lead to illnesses, or even cancer.
Germ-line mutations occur during meiosis and the formation of gametes.
The effect of this mutation may not be felt by the carrier, but is passed onto
their children if the gamete is fertilised. Germ-line mutations are heritable
since they can be passed on/inherited by their offspring.
There are 3 outcomes for genetic mutations
o Sequence still codes for the same amino acids (some amino acids have
more than one code) so there is no change to the polypeptide.
o Sequence codes for at least one different amino acid, which alters the
structure and function of the polypeptide to varying degrees.
o Sequence is changed to include an earlier stop codon, shortening the
polypeptide and often significantly altering its structure and function.

Examples of the effects of types of mutagens

o Radiation Ionises biochemical compounds in cells, forming free radicals
The free radicals cause damage to DNA and proteins (e.g.
breakages in chromosomes)
o Chemicals Some chemicals insert into DNA instead of bases (or substitute
for bases)
Other chemicals insert between bases, causing issues when the
DNA replicates
o UV light Causes thymine bases that are close together on a DNA
polynucleotide chain to bind together, forming thymine dimers.
This causes problems during DNA replication
Chromosomal mutations
o classified according to whether they change the structure of
chromosomes or alter the number of chromosomes in the cell.
o often identified by their karyotype.
o E.g. down syndrome (trisomy 21)- 3 chromosomes in number 21,
Jacob's Syndrome (XYY syndrome) where the chromosome number 23
is XYY, with the inclusion of an extra Y chromosome.
The genetic code is the sequence of bases in a gene and provides the specific
instructions for the synthesis of proteins. Some proteins are the building
material for major structures and organelles within the cell, whereas others
are functional proteins such as enzymes.
Proteins are polymers made up of polypeptides, which are chains of amino
acids.
Only 20 amino acids that occur naturally in human proteins, but they can be
used in millions of different combinations. Each amino acid requires a specific
code, which is made up of the DNA bases A, T, C and G.
Protein Synthesis- where the relevant section (the gene) of DNA is copied into
RNA. The short strands of RNA leave the nucleus and go to a ribosome where
they form a template for an amino acid chain.
Prokaryote- single celled organism which does not have a membrane-bound
nucleus, essentially consisting of free-floating organelles
Eukaryote- any organism whose cells contain a nucleus and other organelles
enclosed within membranes.
Ribosome- the protein builders, they connect amino acids together to form
long chains
Base Sequences
Codon- base triplet which codes for an amino acid, composed of 3
bases(A,U,G,C) e.g. AUG is the met/start codon.
The possibilities for a codon, with there being 4 bases are 4x4x4=64 types of
codons, there are more codons that can code for amino acids than there are
amino acids, so multiple codons code for the same amino acid.
The codons for the amino acids are typically listed using RNA rather than
DNA. All proteins start with the amino acid methionine, which is coded for by
the start codon AUG. They end with the codon TAG or the stop codon.

The base sequence, or base order in DNA is extremely important. Even 1

change in the bases can affect the amino acid produced which affects the
protein produced. They could affect the normal functioning of the organism.
This error could occur during replication, although the aim of replication is to
create exact replicates, mistakes can be made during this process.
Genetic inheritance
Gregor Mendel was an Austrian monk, he carried out the majority of his work
before the structure of DNA was known.
His success in understanding genetic inheritance was due to
o Studying a large sample size, studying a large number of pea plants
(30 000)and a large number of characteristics (7 characteristics)
o Carrying out a large number of crosses- repetition of his experiment to
ensure accuracy
o Using pure breeding lines- eliminating the possibility of the plants not
breeding properly
His experiment essentially involved
o 2 true breeding parental generations. One was a round seed, the other
a wrinkly seed. These seeds had their pollen grains transferred by
hand. The resultant offspring were all rounded seeds. This was odd,
since the parental generation were a mix of half round and half wrinkly
seeds, it appeared that the wrinkly seeds had vanished.
o The seeds of the parental generations (known as F 1) were allowed to
interbreed. Since the seeds were both round, then the resultant
offspring should be round, bearing in mind that the parents were both
round and the parental generation were true-breeding. The resultant F 2
generation contained roughly round and wrinkly seeds. The
wrinkly seeds had somehow formed from 2 round seeded parents.
Mendel proposed that
o There must be factors inside the cell which control the
characteristics-these were later called genes
o 2 copies of the factor that are present in each cell, and control each
characteristic, with one factor from the male parent and one factor
from the female parent
o Each factor is separated before fertilisation (meiosis and gamete
formation) and combines again at fertilisation, but the 2 factors do not
blend.
o The factors which control different characteristics are passed on to the
next generation independently of each other
These proposals expanded into 2 fundamental laws of genetics
o The law of segregation- during meiosis the 2 copies of every gene, that
controls each characteristic, separate and each copy going to the
gamete. The chromosomes recombine at fertilisation.
o The law of independent assortment- when the homologous pairs of
chromosomes segregate, they do so independently of other
chromosomes. When the chromosomes line up in their homologous
pairs, the side each chromosome takes is completely random.
Allele- different forms of the same gene. E.g. the gene is seed shape, and the
allele is wrinkly or rounded

Genotype- the specific combination of alleles

Phenotypes- the physical characteristics of the genotype, noting the
concept of dominant alleles and incomplete dominance. E.g. TT and Tt both
code for a tall pea plant, but have different genotypes.
Homozygous- true breeding individuals, they contain the same genotypes.
E.g. TT and tt
Heterozygous- having different genotypes. E.g. Tt
o One of the alleles in the genotype may be dominant, so its
characteristic is expressed instead of the recessive allele. E.g. Tt, the
T dominates over the t so the Tt genotype is expressed as TT
o The recessive phenotype is only expressed if the genotype contains no
dominant alleles, e.g. tt
Autosomal chromosomes- chromosomes which do not have any effect on
gender differentiation
Sex chromosomes- chromosomes which effect gender (chromosomes
number 23). The possibilities for sex chromosomes are XY and XX.
Monohybrid cross- genetic cross between 2 individuals which are
heterozygous, possible producing homozygous offspring- the results being
tt, TT and Tt.
Test cross- where an individual with the dominant phenotype but unknown
genotypes is crossed with a recessive individual. This takes advantage of the
recessive individual supplying the recessive allele to the offspring, the
offsprings phenotypes determining its genotype, hence determining the
genotype of the dominant phenotype parent.
Sex-linked inheritance
o The genotype of females is XX, the genotype of males is XY
o The X chromosome is much larger than the Y chromosome
o The X chromosome carries genes which are responsible for sexual
characteristics as well as well as other non-sexual characteristics.
o Traits/phenotypes which are carried on a sex chromosome are sexlined. More genes are traits are linked to the X chromosome since it is
much larger than the Y chromosome.
o Males are more likely to show x-linked traits compared to females. This
is due to males only having 1 X-chromosome, whereas females have 2
X-chromosomes. Females have the ability to mask the X-linked trait,
since they could have an allele on the other X-chromosome which
dominates the affected X-chromosome. On the other hand, males only
have 1 X-chromosome, which means that they cannot mask the
affected allele, also the Y chromosome is much smaller, so it cannot
mask the x-linked trait.
o Examples of X-linked traits include red-green colour blindness and
haemophilia.
Red-green colour blindness
o Gene on the X chromosome controls the colour receptors in the retina
of the eye. If the gene is defective, then the person cannot distinguish
red from green.
o Around 8% of males and less than 1% of females have red-green colour
blindness

Haemophilia
o X-linked recessive disease which prevents blood from clotting. This
means that even a small cut could result in extended bleeding and
excessive blood loss or bruising.
o Today, this disease can be treated more easily, with clotting factors
being able to be produced from blood donations or made in the
laboratory.
Carrier- someone who has an allele for the genetic disorder but does not show
the disorder in their phenotype
Pedigrees
o

If the sex is unknown, then the person is represented with a triangle

Offspring are listed in order of birth, the eldest being on the left.

Genome- the full set of genes and alleles found in a species

Gene Technology
Restriction enzymes- proteins which can cut DNA at specific base
sequences. They restrict the growth of other organisms by destroying their
DNA. Their natural role is to protect bacteria from foreign DNA which they cut
up and destroy.
DNA ligases- they attach or link pieces of DNA together. However, they are
less specific compared to restriction enzymes.
Sanger sequencing- artificially replicating DNA with bases that have
radioactive or fluorescent tags attached onto a computer. The DNA with the
tag is analysed by a computer, and reads the tags, records them and
analyses them. Allows for the fast identification of bases
Genetic engineering- the manipulation of a genome of an organism, usually
through altering the base sequence of specific genes or by transferring genes
from one organism to another.


First the genetic sequence is determined

Then it is cut out with the use of restriction enzymes

Then it is inserted into the new organism with DNA ligases. Note:
the new organism does not have to be the same species as the donor
organism.

Organisms with the new, inserted genes are known as transgenic

organisms.

To copy a genetic sequence, the sequence is transplanted into

bacteria, the bacteria multiple rapidly, and the sequences are cut out
again with the same restriction enzymes. This is how the cloning of base
sequences works.
Gene therapy- the process of cutting out faulty genes and inserting in normal
genes. It has been successful in the treatment of cystic fibrosis.
Recombinant DNA- DNA with the new gene, often found in the surrogate
bacteria.

Applications of gene
technologies:

Environmental applications
DNA
profiling is used to
solve criminal
cases.
DNA
profiling used to
identify
the father of a
child
Development of
bacteria containing
genes to break down oil
deposits and mining wastes.
These help to ease the
effects of an oil spill and waste
products from mining.

Agricultural
applications
Crops have been
engineered to be resistant
against pesticides and/or
diseases, so that when pesticides are
sprayed, the
crops are undamaged
Increasing
the nutrient value of cheap crops (e.g.
rice and wheat) can
reduce starvations and
malnutrition in poor
areas.
Genetic screening and
testing

Testing for a variety

of conditions regardless of a
previous family history of
genetic disease.

Helps with the diagnosis

of genetic diseases and
hence intervention

Amniotic fluid
testing- the fluid in the
amniotic sac is
withdrawn using a needle, and
this is tested to indicate if
there are any potential
problems with the baby
Stem cells- undifferentiated cells
which can differentiate
into many different types of
specialised cell types. E.g.
muscle, nerve and blood cells.

There are 2
types of stem cells
Embryonic
stem cells- can
become most
cells types
Adult stem
cells- can only
become certain types
of cells

Adult stem cells are used more commonly and there are no ethical
concerns raised about the use of them
Embryonic ethical concerns

Embryos can be produced by fertilising ova in labs.

The use of embryonic cells is considered unethical by some due to

the collection of stem cells means that the embryo is destroyed.

Some parents may want to choose to have certain embryos

compared to others. E.g. some may want a male or female child, or one
with a certain physical characteristic.

When an embryo is considered a person

Cloning

A clone is an exact copy of something else

It is possible to clone an entire organism by nuclear transfer.


Dolly the sheep was the first cloned mammal
Genetically modified organisms

GM crops pose a threat to bio-diversity, they replace a number of

natural varieties of plants with one variety (the GM plant).

GM plants with a resistance to a certain pest can cause a resistance

in the pest, one which cannot be controlled with current GM, so this is a
major issue.
Chromosomes are made of strands of DNA, DNA has genes encoded onto
them
Gamete- sex cell

Chemistry
Acids in the stomach- NaCl, HCl, KCl
Acidic OceansRespiration
Aerobic Respiration:
glucose + oxygen carbon dioxide + water + energy (stored in an ATP
molecule)
C6H12O6 + 6O2 6CO2 + 6H2O + ATP
Anaerobic Respiration for animals
glucose lactic acid + energy
C6H12O6 2C3H6O3 + energy
Anaerobic Respiration for plants
glucose ethanol + carbon dioxide + energy
C6H12O6 2C2H5OH + 2CO2 + energy
Iron and Steel
Reaction 1

Carbon + Oxygen Carbon Dioxide

C(s) + O2(g) CO2(g)

Exothermic- produces heat

This reaction is used to produce heat to break down the iron ore.
Reaction 2

calcium carbonate calcium oxide + carbon dioxide

CaCO3(s) CaO(s) + CO2(g)

This is a decomposition reaction.

The calcium oxide produced in this process helps to remove some of

the other materials contained in the iron ore by reacting with them.

The carbon dioxide reacts with some of the coke to produce carbon
monoxide (CO).
Reaction 3
carbon + carbon dioxide carbon monoxide
C(s) + CO2(g) 2CO(g)
The carbon monoxide then reacts with the iron ore and takes the
oxygen.
Reaction 4
carbon monoxide + iron oxide carbon dioxide + iron
3CO(g) + Fe2O3(s) 3CO2(g) + 2Fe(s)
Purifies the Iron(II) oxide into pure iron.
Acid

Base

Corrosive, can cause severe burns

Caustic, feels slippery

Taste sour

Tastes bitter

sulfuric acid(H2SO4)- used extensively in

industry and to make other acids. It is used in
car batteries and to clean oxide layers off
metals before they are plated with other

react with fats and oils to

produce soaps.

metals.
Nitric acid(HNO3)- manufacture fertilisers,
plastics, dyes and explosives.

Some bases, such as ammonia

solution, are used in cleaning
agents.

Hydrochloric acid(HCl)- clean metals, bricks

and tiles.

Sodium hydroxide (NaOH) is

used in the manufacture of
soap and paper. It is also used
in drain cleaner and oven
cleaner.

Phosphoric acid(H3PO4)- ingredient in cola

Calcium hydroxide(Ca(OH)2) is
drink, used in industry to produce fertilisers,
used to make plaster and
small amounts are used in drinks to give a
mortar.
distinctive tangy taste. Also preserves the drink
since it kills microorganisms

Indicator substance that changes colour in the presence of an acid or base

e.g. Flavin, litmus paper, universal indicator.
Types of Reactions
Neutralisation: Acid + base salt + water

Acid + metal salt + hydrogen gas

Acid + carbonate salt + water + carbon dioxide

Combustion

fuel + oxygen combustion products + heat

hydrocarbon + excess oxygen carbon dioxide + water

hydrocarbon + limited oxygen carbon monoxide + water

iron + water + oxygen iron (III) oxide [rusting/corrosion]

Corrosion

Metal + Oxygen -> metal oxide (basic oxides)

Corrosion: e.g. rust.

4Fe(s) + 6H2O(l) + 3O2(g) 4Fe(OH)3(s)
Aluminium oxide forms a skin over the top of the metal. Extra
oxygen/moisture cannot get through to the aluminium underneath.
Decomposition: AB + energy -> A + B
e.g. water ---electricity---> Hydrogen + oxygen
Displacement and Precipitation

Motion
Types of Graphs

Position-Time graph
Gradient= velocity
Velocity-Time graph
Gradient= acceleration
Area under graph= displacement
Acceleration-Time graph
Area under curve= velocity

Scalar Quantity- Containing only the magnitude

Vector quantity- contains both magnitude and direction
Distance- how far an object has travelled
Displacement- the relationship between the final position and the initial
position(contains a magnitude and a direction)
Speed- how fast an object is moving
Velocity- the rate of change of displacement over time OR speed in a
particular direction
Acceleration- the rate of change of velocity over time
Average Speed- the total distance over the total time
Instantaneous speed- the speed of an object at that moment in time