Lesson 1 – DNA Replication

CHANGES

For many years, biologists referred to the one gene-one enzyme hypothesis. It was
believed that each gene controlled the production of a single protein.
This was changed to the one gene-one protein hypothesis because many proteins are
structural proteins, not enzymes
Since some proteins consist of several polypeptide chain that are linked together, the
hypothesis was changed again. This time one gene-one polypeptide seemed more
accurate
As a result of Human Genome Project, the one gene-one polypeptide hypothesis has had
to be changed again! We now know that a gene can produce more than one polypeptide
depending upon how the information in the gene is read.

RNA vs. DNA

✓ RNA contains the sugar ribose
✓ RNA contains the base uracil
✓ RNA is usually single stranded
✓ RNA is a short: one gene long at most
✓ DNA contain deoxyribose
✓ DNA contains thymine instream
✓ DNA is usually double stranded
✓ DNA is long, containing many
genes

RNA is an Intermediary Between DNA and a Polypeptide Chain

• RNA is central to the flow of genetic information. Three types of RNA interact to
synthesize proteins:
❖ Messenger RNA (mRNA) – carries the information that specifies a
protein. Each of three mRNA bases in a row forms a codon, which is a
genetic “code word” that corresponds to one amino acid
❖ Ribosomal RNA (rRNA) – combines with proteins to form a ribosome, the
physical location of protein synthesis. Some of rRNA helps to correctly align
the ribosome and mRNA, and others catalyze formation of the bonds between
amino acids in the developing protein
❖ Transfer RNA (tRNA) – molecules are “connectors” that bind an mRNA
code to the one end and a specific amino acid to the ribosome at the correct
spot along the mRNA molecule
MAJOR TYPES OF RNA
Molecule Typical Number of Function
Nucleotides
mRNA 500-3000 Encodes amino acid
sequence
rRNA 100-3000 Associates with proteins to
form ribosomes, which
structurally support and
catalyze protein synthesis
tRNA 75-80 Binds mRNA codon on one
end and an amino acid on
the other, linking a gene’s
message to the amino acid
sequence it encodes

The flow of information in the cell starts at DNA,

which replicates to form more DNA. Information is
then “transcribed” in to RNA, and then it is
“translated” into protein. The proteins do most of
the work in the cell.
Information does not flow in the other direction.
This is a molecular version of the incorrectness of
“inheritance of acquired characteristics.” Changes in
proteins do not affect the DNA in a systematic
manner (although they can cause random changes
in DNA).

DUPLICATION

➢ Before a cell can divide, the DNA in the nucleus of

the cell must be duplicated
➢ Since the DNA molecule consists of two
complimentary strands, if those two strands
separate and the right conditions are present, two
new strands are the compliments of the originals
will be produced
➢ Each new DNA molecule will consist of one old
strand, and a new complimentary strand
 ➢ The gray strands in the figure to the right are new strands in the process of
being assembled Assembling the New Bases
The term semiconservative replication means that in the new DNA molecule there
is one old and one new strand

Duplication needs the following participants:

❖ Helicase – enzymes that unwind “unzip” the DNA

❖ Binding Proteins – prevents the two single strand from rejoining each other
❖ Primase – an enzyme that builds short complementary piece of RNA, called
RNA primer attracts the DNA
polymerase
❖ DNA Polymerase – the enzyme
that adds new DNA nucleotides
that are complementary to the
bases on each exposed strand
❖ Ligase – an enzyme that
removes each RNA primer and
replaces it with correct DNA
nucleotides one the new strand of
DNA is in place

STEPS IN DNA REPLICATION

1. The first step in DNA replication is to ‘unzip’ the double helix structure of the
DNA molecule
2. This is carried out by an enzyme called helicase which breaks the hydrogen
bonds holding the complementary bases of DNA together (A with T, C with G)
3. The separation of the two single strands of DNA creates a ‘Y’ shape called a
replication ‘fork’. The two separated strands will act as templates for making
the new strands of DNA
4. One of the strands is oriented in the 3’ to 5’ direction (towards the replication
fork), this is the leading strand. The other strand is oriented in the 5’ to 3’
 direction (away from the replication fork), this is the lagging strand. As a result
of their different orientations, the two strands are replicated differently.

LEADING STRAND

➢ Short piece of RNA called a primer (produced by an enzyme called primase)

comes along and binds to the end of the leading strand. The primer acts as the
starting point for DNA synthesis.
➢ DNA polymerase binds to the leading strand and then ‘walks’ along it, adding
new complementary nucleotide bases (A, C, G, and T) to the strand of DNA in the
5’ to 3’ direction
➢ This sort of replication is called continuous

LAGGING STRAND

➢ Numerous RNA primers are made by the primase enzyme and bind at various
points along the lagging strand
➢ Chunks of DNA, called Okazaki fragments, are then added to the lagging
strand also in the 5’ to 3’ direction
➢ This type of replication is called discontinuous as the Okazaki fragments will
need to be joined up later

DUPLICATION

➢ Since the DNA molecule is very large, there

must be a way to copy it faster then just
unwinding from one end to the other
➢ This happens when the DNA molecule separates
at many sites, forming thousands of replication
bubbles. This allows parts of the DNA message
be replicated simultaneously in many locations
➢ DNA polymerase adds new nucleotides, while
DNA ligase joints the DNA segments together
➢ The important idead is that and exact
duplication of the DNA message is required, so
that each new cell in the body has the same set
of genetic instructions as the cells the preceded
it
➢ This also insures that every new generation of individuals has the
same genetic information as his/her parents
DNA carries information that can be used to construct the proteins which
form structures and regulate the body’s activities

• Protein synthesis involves two processes:

transcription and translation
• In transcription, the DNA message is converted
into an RNA molecule
• In translation, the RNA message is used to
assemble amino acids in to a protein chain

Lesson 2 – Protein Synthesis

TRANSCRIPTION

➢ Produces an RNA copy of one gene

➢ In transcription, RNA nucleotide bases bind with exposed complementary bases
on the template strand, which is the strand in DNA molecule that is actually
copied to RNA
➢ The process occurs in three stages:
• Initiation
• Elongation
• Termination

INITIATION

➢ Enzymes unzip the DNA double helix, exposing the template strand
➢ RNA polymerase (the enzyme that builds an RNA chain) binds to the promoter, a
DNA sequence that signals the gene’s start

ELONGATION

➢ RNA polymerase moves along the DNA template strand in a 3’-to-5’ direction,
adding nucleotides only to the 3’-end of the growing RNA molecule

TEMINATION

➢ A terminator sequence signals the end of the gene

 ➢ Upon reaching the terminator sequence, the RNA polymerase enzyme separates
from the DNA template and releases the newly synthesized RNA
➢ The DNA molecule then resume its usual double-helix shape
➢ As the RNA molecule is synthesized, it curls into a three-dimensional shape
dictated by complementary base pairing within the molecule.
➢ The final shape determines whether the RNA functions as mRNA, tRNA, or rRNA
➢ The observation that the cell’s DNA encodes all types of RNA – not just mRNA –
has led to debate over the definition of the word gene
➢ Originally, a gene was defined as any stretch of DNA that encodes one protein.
More recently, however, biologist have expanded the definition to include any
DNA sequence that is transcribed
➢ The phrase gene expression can therefore mean the production of either a
functional RNA molecule or a protein

mRNA is Altered in the Nucleus of Eukaryotic Cells

❖ In bacteria and archaea, ribosomes may begin translating the mRNA to a protein
before transcription is even complete
❖ In eukaryotic cells, however, the presence of the nuclear membrane prevents one
mRNA from being simultaneously transcribed and translated
❖ Moreover, in eukaryotes, mRNA is usually altered before it leaves the nucleus to
be translated
❖ 5’ Cap and Poly A tail
• After transcription, a short sequence of modified nucleotides, called a cap,
is added to the 5’ end of the mRNA molecule. At the 3’ end, 100 to 200
adenines are added, forming a “Poly A tail.”
• Together the cap and poly A tail enhances translation by helping
ribosomes attach to the 5’ end of the mRNA molecule
• The length of the poly A tail may also determine how long an mRNA last
before being degraded
❖ Intron Removal
• In archaea and in eukaryotic cells, only part of the an mRNA
molecule is translated into amino acid sequence
• mRNA consist of alternating sequences called introns and exons
▪ Introns – are portions of the mRNA that are removed before
translation.
• The word intron is short for intragenic regions, where intra- means
“within” and -genic refers to the gene
• Small catalytic RNA’s and proteins remove the introns from the
mRNA
 ▪ Exons – portions of an mRNA molecule that are actually expressed
or that exit the nucleus
• Exons are spliced together to form the mature mRNA that
leaves the nucleus to be translated

CLEANING UP THE MESSAGE

➢ When the genetic message is copied to make mRNA, the messages contains
unwanted base sequences
➢ The ‘junk’ sequence (called introns) are removed from the message and the
remaining sequences (exons) are linked together to produce a sequence of codons
that will translate into a polypeptide
➢ This process occurs before the message leaves the nucleus

TRANSLATION BUILDS THE PROTEINS

Translation – the actual construction of the proteins – requires the following

participants:

- mRNA: this product of transcription carries the genetic information that encodes
a protein, with each three-base codon specifying one amino acid
- tRNA: this “bilingual” molecules binds to an mRNA codon and to an amino acid
• The anticodon is a three-base loop that is complementary to one
mRNA codon. The other end of the tRNA molecules form a covalent
bond to the amino acid corresponding to the codon
- Ribosome: the ribosome, built of rRNA and proteins, anchors mRNA during
translation
• Each ribosome has a large and small subunit that join at the initiation of
protein synthesis

THE GENETIC CODE

❖ Virtually all organisms share the same genetic code

“unity of life”
❖ There are 64 (4x4x4) possible triplet codes, but only
20 amino acids
❖ As seen in the table, more than 1 triplet may code
for the same amino acid. This is no problem, as long
as no triplet can code for more than one amino acid
❖ Note that several codons can also act as start (AUG)
or stop (UAA) signals
 ❖ The genetic code is written in the sequence of the 4 bases of DNA: A, T, C, and G
❖ Three bases read in sequence specify one of the 20 amino acids found in protein
molecules
❖ A codon is the 3-base sequence of an amino acid
❖ The message in the DNA is transcribed into an RNA molecule, and then
translated into a polypeptide

WHERE OH WHERE CAN THE AMINO ACIDS BE?

❖ A second type of RNA is transfer RNA, whose

function is to attach to a specific amino and bring
that amino acids to the site where polypeptides
are being constructed
❖ This RNA strand is twisted and bonded into the
shape seen on the right
❖ One end of the molecule attached to a specific
amino acid
❖ The other end has an exposed sequence of 3bases.
These are called the anticodon
❖ How many kinds of tRNA must there be?

YOU MUST KNOW YOUR BASE PAIRS!!

❖ If you said 20 types of tRNA you are wrong!

❖ There must be a different tRNA molecule for each of the possible triplets. This
means 64 anticodons
❖ The anticodons of the tRNA each have a complimentary codon in the mRNA.
For example, the codon AUG would be the compliment of the anticodon UAC
CODON CHART

THE ROLE OF RIBOSOMES

❖ The third type of RNA is ribosomal RNA (rRNA)

❖ Ribosomes are ‘decoding’ units of the cell
❖ Each ribosome consists of two subunits, and is an assemblage of rRNA and
proteins
❖ Ribosomes have binding sites for both tRNA and mRNA molecules
READING THE MESSAGE

❖ An mRNA molecule attaches to a ribosome

❖ As the ribosome moves along the mRNA, 3-base codons are exposed one at a time
❖ A tRNA with an anticodon of the mRNA temporarily bonds with the mRNA
❖ The ribosome positions the molecules so that this bonding occurs
❖ As the ribosome continues its journey along the mRNA, additional tRNAs bring
their a.a. to the site of peptide synthesis

ELONGATION OF THE CHAIN

❖ As new amino acids are brought to the ribosome, the growing peptide chain is
attached to the new amino acid by a peptide bond
❖ Elongation of the chain continues until a stop codon is encountered. At that
point, the peptide chain is released from the tRNA
❖ A single mRNA can be read repeatedly to make many copies of a polypeptide
❖ Once a tRNA gives up its amino acid, it can return to the cytoplasm and attach to
another of its specified amino acid

TRANSLATION OCCURS IN 3 STEPS

Initiation

1. The leader sequence at the 5’ end of the mRNA molecule bonds with a small
ribosomal subunit
2. The first mRNA codon to specify an amino acid is usually AUG, which attracts a
tRNA that carries the amino acid methionine
3. This methionine signifies the start of a polypeptide
4. A large ribosomal subunit attaches to the small subunit to complete initiation

Elongation

5. A tRNA molecule carrying the second amino acid then binds to the second codon.
Amino acids are then connected by a covalent bond known as a peptide bond
6. With the protein called elongation factors, the polypeptide grows one amino acid
at a time, as tRNA’s continue to deliver their cargo

Termination

7. Elongation halts at a “Stop” codon (UGA, UAG, or UAA)

 8. No tRNA correspond to these stop codons. Instead, proteins called release factors
bind to the stop codon, prompting the release of the last tRNA from the ribosome
9. The ribosomal subunit separate from each other and are recycled, and the new
polypeptide is released.

Translation

10. Protein synthesis can be very speedy

• A plasma cell in the human immune system can manufacture 2000 identical
antibody proteins per second
• Transcription produces multiple copies of each mRNA, and dozens of
ribosomes may simultaeneously bind along the length of a single mRNA
molecule

ERRORS IN PROTEIN FOLDING

❖ Alzheimer’s Disease
➢ Associated with a protein called amyloid that fold improperly and then forms an
abnormal mass in brain cells
❖ Likewise, mad cow disease and similar conditions in sheep and humans are
caused by abnormal clumps of misfold proteins called prions in nerve cells

❖ Some proteins must be altered in other ways before the become functional
➢ Insulin which is 51 amino acids long, is initially translated as the 80-amino-acid
polypeptide proinsulin. Enzymes cuts proinsulin to form insulin

❖ A different type of modification occurs when polypeptides join to form larger

protein molecules
➢ Hemoglobin in blood cells is consit of four types of polypeptide chains (2 alpha
and 2 beta) encoded by separate genes

SOME POISONS DISRUPT PROTEIN SYNTHESIS

Some poisons kill by interfering with respiration. Some poisons inhibits protein
synthesis; a cell that cannot make proteins quickly dies

▪ Amanatin – this toxin occurs in the “death cup mushroom.” Amanatin inhibits
RNA polymerase, making transcription impossible
▪ Diphtheria Toxin – bacteria called Corynebacterium diphtheriae secrete a
toxin that causes a respiratory illness
 ▪ Antibiotics – Clindamicyn, chloramphenicol, tetracyclines, and gentamicin are
all antibiotics that binds to bacterial ribosomes
▪ Ricin – derived from the seeds of the castor bean plant, ricin is a potent natural
poison that consist of two parts. One part binds to a cell, and the other enters the
cell and inhibits protein synthesis
▪ Trichothecenes – fungi in genus Fusarium produce toxin Trichothecenes.
Biological weapons. Somehow, it interferes ribosomes.
5. Macapuno trait in coconuts
MODYFYING TECHNIQUE
Lesson 3 – Recombinant DNA Technology

ENHANCED TRAIT 1. Classical breeding

2. Classing breeding
1. Kobe/Wagyu Beef (beef with good 3. Recombinant DNA Technology
fat distribution) 4. Recombinant DNA Technology
2. Guapple (larged sized guava) 5. Classical breeding
3. Human insulin-producing bacteria
4. Flavor (delayed-ripening tomatoes)
SELECTIVE BREEDING

❖ Breed only those plants or animals with desirable traits

❖ People have been using selective breeding for 1000’s of years with farm crops and
domesticated animals

RECOMBINANT DNA

❖ The ability to combine the DNA of one organism with the DNA of another
organism
❖ Recombinant DNA technology was first used in the 1970’s with bacteria

RECOMBINANT BACTERIA (Steps)

1. Remove bacterial DNA (Plasmid)

2. Cut the bacterial DNA with
“restriction enzymes”
3. Cut the DNA from another
organism with “restriction
enzymes”
4. Combine the cut pieces of DNA
together with another enzyme and
insert them into bacteria
 5. Reproduce the recombinant bacteria
6. The foreign genes will be expressed in the bacteria

BENEFITS OF RECOMBINANT BACTERIA

◼ Bacteria can make human insulin or human growth hormone ◼

Bacteria can be engineered to “eat” oil spills

THE DNA OF PLANTS AND ANIMALS CAN ALSO BE ALTERED

Plants

➢ Disease-resistant and insect-resisteant crops

➢ Hardier fruit
➢ 70-75% of food in supermarket is genetically modified

How to Create a Genetically Modified Plant

1. Create recombinant bacteria with desired gene

2. Allow the bacteria to “infect” the plant cells
3. Desired gene is inserted into plant chromosomes

GENETICALLY MODIFIED ORGANISMS ARE CALLED TRANSGENIC ORGANISMS

Transgenic Animals

❖ Mice – used to study human immune system

❖ Chickens – more resistant to infections
❖ Cows – increase milk supply and leaner meat
❖ Goats, sheep, and pigs – produce human proteins in their milk

TRANSGENIC GOAT

Human DNA in a Goat Cell This goat contains a

human gene that
g agent. The
 blood clotting agent can be harvested in
the goat’s milk

HOW TO CREATE A TRANSGENIC ANIMAL

Desired DNA is added to an egg cell

CLONING

POLYMERASE CHAIN REACTION

❖ PCR is a means to amplify a particular piece of DNA o Amplify = making

numerous copies of a segment of DNA
❖ PCR can make billions of copies of a target sequence of DNA in a few hours
❖ PCR was invented in the 1984 as a way to make numerous copies of DNA
fragments in the laboratory

DNA REPLICATION VS PCR

PCR is a laboratory version of DNA replication in cells

❖ The laboratory version is commonly called “in

vitro” since it occurs in a test tube while “in
vivo”signifies occurring in a living cell.

The DNA, DNA polymerase, buffer, nucleoside triphosphates,

and primers are placed in a thin-walled tube and then these
tubes are placed in the PCR thermal cycler
3 MAIN STEPS OF PCR

• The basics of PCR is temperature changes and the effect that these changes have
on the DNA
• In a PCR reaction, the following series of steps is repeated 20-40 times o (note:
25 cycles usually takes 2 hours and amplifies the DNA fragment of interest
100,000 fold)
Step 1: Denature DNA
➢ At 950C, the DNA is denatured (i.e., the two strands are separated)
Step 2: Primers Anneal
➢ At 40oC-65oC, the primers anneal (or bind to) their complementary sequences on
the single strands of DNA
Step 3: DNA polymerase Extends the DNA chain
➢ At 72oC, DNA Polymerase extends the DNA chain by adding nucleotides to the 3’
ends of the primers

APPLICATIONS OF PCR

Primers can be created that will only bind and amplify certain alleles of genes or
mutations of genes

✓ This is the basis of genetic counseling and PCR is used as part of the diagnostic
tests for genetic diseases
Some diseases that can be diagnosed with the help of PCR:

✓ Huntington’s disease
✓ Cystic fibrosis
✓ Human immunodeficiency virus

PCR APPLICATIONS TO FORENSIC SCIENCE

PCR can be used to amplify highly variable regions of human genome. These regions
contain runs of short, repeated sequences (known as variable number of tandem repeat
(VNTR) sequences). The number of repeats can vary from 4-40 in different individuals.
Primers are chosen that will amplify these repeated areas and the genomic fragments
generated give us a unique “genetic fingerprint” that can be used to identify an
individual.

➢ Paternity suits – Argentina’s Mothers of the plaza and their search for abducted
grandchildren
➢ Identifying badly decomposed bodies or when only body fragments are found –
World trade center, Bosnian, Iraq & Rwandan mass graves

Lesson 4 – Taxonomy
To study the diversity of life, biologists use a classification system to name organisms
and group them in a logical manner.
Taxonomy – Discipline of classifying organisms and assigning each organisms a
universally accepted name
Nomenclature – naming tool. Nomenclature only follows taxonomy

WHY COMMON NAMES DON’T WORK

Common names vary among languages. Example:

United Kingdom – buzzard refers to a hawk HISTORY
United States – buzzard refers to a vulture Aristotle

➢ 2000 years ago, Aristotle (382

BC-322BC) was the first
taxonomist
➢ Aristotle divided organisms into
plants & animals
 ➢ He subdivided them by their habitat Carolus Linnaeus (1707 – 1778)
– land, sea, or air dwellers
➢ Classified organisms by their
➢ Early scientists used common names
structure
to identify organism
➢ Created the system of naming we
➢ Examples of common names:
use today
seahorse, starfish, sealion,
jellyfish ➢ His classification system includes
7 levels
➢ In taxonomy, a group or level or
BINOMIAL NOMENCLATURE organization is called taxonomic
catefory or taxon
➔ “Bi” mean 2 ➢ To avoid confusion, Carolus
➔ “nomial” means naming Linnaeus devised a namin system
based on physical characteristics
(structures)
➔ Nomenclature means “ the system of naming”
➔ Defined: in binomial nomenclaure, each species is assigned a two-part
scientific name
➔ Example: Polar Bear is Ursus maritimus o Ursus: genus – ursus contains 5
other kinds of bears
o maritimus: species – the Latin word, maritimus, refers to
the sea o Polar bears often live on pack ice that floats in the
sea

Genus – a group of closely related species (example: wolf, dog, coyote, golden jackal)
Species – group of similar organisms that can breed and produce fertile offspring

Kingdom – largest taxonomic group consisting of closely related phyla

Phylum – group of closely related classes
Class – group of similar orders
Order – group of similar families
Family – group of genera (genus) that share many characteristics
Genus – group of closely related species that share common
Species – group of organisms that can interbreed to produce fertile
offspring The level of classification that contains organisms most
closely related is species.
The level of classification that contains organisms least closely related is kingdom.

Example: Polar Bear What they mean

Kingdom – Animalia Species – maritimus (lives in marine
environment)
Phylum – Chordata
Genus – Ursus (kind of bear)
Class – Mammalia
Family – Ursidae (larger catergory of
Order – Carnivora
bears)
Family – Ursidae
Order – Carnivora (meat-eating
Genus – Ursus animals)

Species – maritimus Class – Mammalia (warm-blooded, hair,

& milk)
Phylum – Chordata (vertebrates)
Kingdom – Animalia (there are 5
kingdoms

HOW TO REMEMBER

King Philip Came Over For Green Salad

Kingdom Phylum Class Order Family Genus Species

RULES

1. Uniqueness: every name has to be unique

2. Universality: Zoologists have adopted, by internation agreement, a single
language to be used on a worldwide basis. All animals are given a generic
(common name) and specific name in Latin (scientific name)
3. These names are in italics or are underlined (i.e. Homo sapiens or Homo
sapiens)
4. Genus and species are used in the organism’s name
5. This system of using 2 name to identify an organisms is called binomial
nomenclature
6. The binomial name is also known as the scientific name
GENUS SPECIES

If these three species belong to the

same genus, they are descended
from a common ancestor.

LINNAEUS VS. MODERN ❖ 5 kingdoms

CLASSIFICATION ❖ Based on physical similarities
AND genetic similarities
Linnaeus
❖ Uses observations, knowledge of
❖ 2 kingdoms organisms, molecular clocks, and
❖ Based on physical similarities other genetic techniques
❖ Uses only biologists observations
and knowledge of organisms
Modern
A PROBLEM WITH TRADITIONAL CLASSIFICATION

• Traditional classification systems relied on body structure comparisons only

• Due to convergent evolution, organisms that are quite different from each
other evolve similar body structures

Convergent Evolution: process by which unrelated organisms independently evolve

similarities when adapting to similar environments
Example: The Crab, The Barnacle, & The Limpet

• The barnacle and the limpet have similarly shaped shells & look alike
• The crab has a very different body form
• Based on anatomy, the barnacle & limpet could be classified together and the
crab in a different group

MODERN CLASSIFICATION

Five Kingdom System: Older system, lumps all prokaryotic species into one kingdom:
Monera

• Animal, Plant, Protist, Fungi, Monera

WHERE DO VIRUSES GO?

Viruses: particles of nucleic acid, protein, and in some cases lipids that can reproduce
ONLY by infecting living cells.

➔ Viruses are made of a core of either DNA or RNA surrounded by a

protein coat
 ➔ Viruses are not considered alive because they don’t have ALL the
characteristics of life
➔ Example: they can’t reproduce independently.
T4 Bacteriophage

➔ A bacteriophage is a virus which infects bacteria

EVOLUTIONARY CLASSIFICATION

Biologists now group organisms into categories that represents lines of evolutionary
descent, not just physical similarities
Evolutionary Classification – the strategy of grouping organisms together based on
their evolutionary history

CLASSIFICATION USING CLADOGRAMS

Cladogram – a diagram that shows the evolutionary relationships among a group of

organism

DICHOTOMOUS KEYS

▪ In the field, biologists use dichotomous keys to identify organisms

▪ Dichotomous Key – a chart that identifies organisms based on their
characteristics. It’s used by excluding organisms based on their OBSERVABLE
features

PHYLOGENY

▪ Phylogeny is the presumed evolutionary

history of an organism
 ▪ The phylogeny of related organisms can be illustrated using a phylogenic tree
▪ All life forms are related by common ancestry and descent. The construction of
phylogenies provides explanations of the diversity seen in the natural world
▪ Phylogenies can be based on morphological data, physiological data, molecular
data or
all three. Today, phylogenies are usually constructed using DNA sequence data
▪ In molecular phylogenies, characters are typically nucleotide positions in
gene sequence, and each position can possess four Character States: A, C, G,
or T

MITOCHONDRIAL DNA ARE USED

Four properties make mitochondrial genomes especially suitable for identifying species:
Copy number. There are 100-10,000 more copies of mitochondrial than nuclear DNA
per cell, making recovery, especially from small or partially degraded samples, easier
and cheaper.
Relatively few differences within species in most cases. Small intraspecific and
large interspecific differences signal distinct genetic boundaries between most species,
enabling precise identification with a barcode.
Introns, which are non-coding regions interspersed between coding regions
of a geme, are absent from mitochondrial DNA of most animal species,
making amplification straightforward. Nuclear genes are often interrupted by
introns, making amplification difficult or unpredictable.
Greater differences among species. On average 5- to 10 fold higher in
mitochondrial than in nuclear genes. Thus, shorter segments distinguish among species,
and because shorter, less expensively.
Barcodes affirm the unity of the species Homo sapiens. Comparison show we
differ from one another by only 1 or 2 nucleotides out of 648, while we differ from
chimpanzees at 60 locations and gorillas at 70 locations.

MATERIAL:

double-helix activity

INTRODUCTION

In doing the Double Helix Activity students will read about the way nucleotides are built in a
basic sense, the similarities and differences between DNA and RNA nucleotides, the
locations in the cell where they can be found, and what their functions are. Additionally,
there is a fair amount of color-coding of nucleotides and how they are built (sugar-
phosphate-base) which will be relevant as we unpack the process of protein manufacture.
All of the remaining instruction in this series featuring the "Central Dogma" depends on this
basic understanding.

The overarching question students will grapple with is, "How does the
invisible genotype (DNA-based gene segment coded as "AA" or "Aa" for example)
transform into the visible phenotype (such as hair or eye color)?

DNA - The Double Helix

Recall that the nucleus is a small spherical, dense body in a cell.  It is often called the
"control center" because it controls all the activities of the cell including cell reproduction,
and heredity. Chromosomes are microscopic, threadlike strands composed of the chemical
DNA (short for deoxyribonucleic acid).  In simple terms, DNA controls the production of
proteins within the cell.  These proteins in turn, form the structural units of cells and control
all chemical processes within the cell.  Think of proteins as the the building blocks for an
organism, proteins make up your skin, your hair, parts of individual cells. How you look is
largely determined by the proteins that are made. The proteins that are made is determined
by the sequence of DNA in the nucleus.
Chromosomes are composed of genes, which is a segment of DNA that codes for a
particular protein which in turn codes for a trait.  Hence you hear it commonly referred to as
the gene for baldness or the gene for blue eyes.  Meanwhile, DNA is the chemical that
genes and chromosomes are made of. DNA is called a nucleic acid because it was first
found in the nucleus.  We now know that DNA is also found in organelles, the mitochondria
and chloroplasts, though it is the DNA in the nucleus that actually controls the cell's
workings.
In 1953, James Watson and Francis Crick established the structure of DNA.  The shape of
DNA is a double helix, which is like a twisted ladder. The sides of the ladder are made of
alternating sugar and phosphate molecules.  The sugar is deoxyribose.

The rungs of the ladder are pairs of 4 types of nitrogen bases. The bases are known by their
coded letters A, G, T, C.   These bases always bond in a certain way.  Adenine will only bond
to thymine.  Guanine will only bond with cytosine. This is known as the "Base-Pair Rule". The
bases can occur in any order along a strand of DNA. The order of these bases is the code
that contains the instructions. For instance ATGCACATA would code for a different gene
than AATTACGGA. A strand of DNA contains millions of bases.

Note that that the bases attach to the sides of the ladder at the sugars and not the phosphate.

The DNA helix is actually made of repeating units called nucleotides. Each nucleotide
consists of three molecules: a sugar (deoxyribose), a phosphate which links the sugars
together, and then one of the four bases. Two of the bases are purines - adenine and
guanine.  The pyrimidines are thymine and cytosine. Note that the pyrimidines are single
ringed and the purines are double ringed.

The two sides of the DNA ladder are held together loosely by hydrogen bonds. The DNA
can actually "unzip" when it needs to replicate - or make a copy of itself. DNA needs to copy
itself when a cell divides, so that the new cells each contain a copy of the DNA. Without
these instructions, the new cells wouldn't have the correct information. The hydrogen bonds
are represented by small circles.

Messenger RNA

So, now, we know the nucleus controls the cell's activities through the chemical DNA, but
how?  It is the sequence of bases that determine which protein is to be made.  The
sequence is like a code that we can now interpret.  The sequence determines which proteins
are made and the proteins determine which activities will be performed.  And that is how
the nucleus is the control center of the cell.  The only problem is that the DNA is too big to
go through the nuclear pores.  So a chemical is used to to read the DNA in the nucleus. 
That chemical is messenger RNA.   The messenger RNA  (mRNA) is small enough to go
through the nuclear pores.  It takes the "message" of the DNA to the ribosomes and "tells
them" what proteins are to be made.  Recall that proteins are the body's building blocks.
Imagine that the code taken to the ribosomes is telling the ribosome what is needed - like a
recipe.

Messenger RNA is similar to DNA, except that it is a single strand, and it has no thymine.
Instead of thymine, mRNA contains the base Uracil. In addition to that difference, mRNA has
the sugar ribose instead of deoxyribose. RNA stands for Ribonucleic Acid.
The Blueprint of Life

Every cell in your body has the same "blueprint" or the same DNA. Like the blueprints of a
house tell the builders how to construct a house, the DNA "blueprint" tells the cell how to
build the organism.   Yet, how can a heart be so different from a brain if all the cells contain
the same instructions?   Although much work remains in genetics, it has become apparent
that a cell has the ability to turn off most genes and only work with the genes necessary to
do a job.  We also know that a lot of DNA apparently is nonsense and codes for nothing. 
These regions of DNA that do not code for proteins are called "introns", or sometimes "junk
DNA". The sections of DNA that do actually code from proteins are called "exons".

Why is RNA necessary to act as a messenger?  Why can't the code be taken directly from
the DNA?

Answer text
Because DNA is too big to go through nuclear pores so RNA is necessary to read the DNA
in the nucleus and act as a messenger sending the "message" of the DNA to the ribosomes
and "tells them" what proteins are to be made.

How do some cells become brain cells and others become skin cells, when the DNA in ALL the
cells is exactly the same.  In other words, if the instructions are exactly the same, how does one
cell become a brain cell and another a skin cell?
Answer text
In studying genetics, it has already observed and determined that a cell has the ability to
turn off most genes and only work with the genes necessary to do a specific job. The cells
that are compatible or useful with the genes in brains will become a brain cell. Likewise, the
DNA cell which is deem needed for the genes in the skin will be skin cells.

Why is DNA called the "Blueprint of Life"?

Answer text
Like the typical blueprint which engineers used as guide on how to build a house, the DNA
tells the cell how to build the organism that is why it is called as the "Blueprint of Life".