General Biology 2 Reviewer

Topic 1: Recombinant DNA Technology

Classical Breeding: mating with organisms with desirable traits
Genetic Engineering: process of altering the DNA

Discovery of DNA Function

1. Johannes Friedrich Miescher – 1st person to describe and extract DNA

2. Fred Griffith – transferred hereditary material from dead cells to live cells; he used two strains of
Streptococcus pneumoniae in his experiment
Mice A – injected with live R cells, lived
Mice B – injected with live S cells, died
Mice C – injected with killed S cells, died
Mice D – injected with killed S cells and live R cells died, live S cells are found in the blood, harmless
bacteria can become transformed into disease-causing bacteria by a bacteria transformation factor

3. Oswald Avery and Maclyn McCarty – concluded that DNA is the transforming principle

4. Alfred Hershey and Martha Chase – radioactive phosphorus (32P) and radioactive sulfur (35S)
were used; bacteriophages transfer their DNA, not their coat proteins, into their hosts; concluded that
DNA, not protein, is the material that stores hereditary information

5. Rosalind Franklin – used x-ray crystallography to determine many aspects of DNA’s structure

6. James Watson and Francis Crick – constructed the DNA double helix model

DNA Structure
DNA – deoxyribonucleic acid; consist of 5-C sugar (deoxyribose), 3 phosphate groups, 1 of 4 nitrogen-
containing bases (purines: adenine, guanine; pyrimidines: thymine, cytosine)

RNA – adenine, guanine, thymine, uracil

Chargaff”s Rule
1st Rule: A=T, G=C
 The hydrogen bonding of cytosine to guanine is an example of complementary base pairing.
2nd Rule: the proportion of adenine and guanine differs among species

Enzymes of DNA Replication

Helicase – break hydrogen bonds and unwind the two strands of the DNA molecule prior to replication
Topoisomerase – untwists the double helix
DNA polymerase – joins free nucleotides into a new strand of DNA
DNA ligase – joins DNA segments on the discontinuous strand
DNA primase – makes primer

Okazaki fragments – are short sections of DNA formed at the time of discontinuous synthesis of the
lagging strand during replication of DNA

Leading strand – synthesized by adding nucleotides to the 3’ end of the growing strand, replicated
continuously
Lagging strand – synthesized by adding nucleotides to the 5’ end, discontinuous replication

Semi-conservative DNA replication – consist of one old strand and one new strand

Mutations
 Can occur as DNA replication errors, can be passed on to the next generation, can’t be repaired after
replication, it is not always dangerous
Agents of DNA Damage
1. Electromagnetic agents – ionizing radiation, UV light
2. Chemical agents – carcinogenic chemicals, environmental pollutants

Cloning – asexual reproduction or embryo splitting

 Somatic cell nuclear transfer (SCNT) – a laboratory strategy for creating a viable embryo from a
body cell and an egg cell
 Therapeutic cloning – to produce human embryos for research purposes
Surrogate mother – for the incubation and carrying the baby until birth

Recombinant DNA Technology (rDNA Technology)

 This is the first step to DNA cloning
 Identification, isolation, and insertion of a desired gene/target gene

Tools in rDNA Technology

1. Target DNA – gene of interest
2. Restriction enzyme – cut DNA into fragments, naturally found in certain bacteria
3. DNA cloning vectors – carries target gene into host cell; bacteriophage: viruses that affect
bacteria; plasmids: small, circular molecule in bacteria that contain genes resistant to certain
antibiotics
4. Host cell – bacterial cell that allows cloning vector to replicate within it
5. Modifying enzymes – DNA ligase, Taq polymerase

Stages in rDNA Technology

1. Selection and isolation of target gene
2. Insertion of a target gene to a vector
3. Introduction of a vector into a target host - transformation
4. Amplification of the target gene by the host cell

Polymerase Chain Rection (PCR)

 Uses heat-resistant DNA polymerase (Taq polymerase) to produce billion of copies of DNA fragments
 Used for the amplification of a gene in vitro (in laboratory)

5 Core Ingredients of PCR

1. DNA template to be copied
2. Primers
3. dNTPs (DNA nucleotide bases)
4. Taq polymerase enzyme
5. Buffer

3 Main Stages of PCR

1. Denaturing – DNA is heated to separate it
Denaturation – is the process to separate two DNA strand by increasing the temperature in
Polymerase Chain Reaction

2. Annealing – temperature is lowered to enable the DNA primers to attach to the template DNA
 When two DNA pieces cut with the same restriction enzyme are combined, the sticky ends will
associate by complementary base pairing and hydrogen bonds

3. Extending – new strand of DNA is made by the Taq polymerase

Genetic engineering
 DNA is manipulated and moved from one source to another

Examples of GMOs
a. Bt Corn – have bacterial insecticide gene that acts as its protection from pests
b. Flavr Savr Tomatoes – meant to be harvested ripe for increased flavor for long-distance shipping
c. Golden Rice – a new type of rice that contains beta carotene
d. Aqua Advantage Salmon – to reach a growth marker important to the aquaculture industry more
rapidly than its non-GE farm-raised Atlantic salmon counterpart
e. Insulin Production - using recombinant DNA to produce human hormones from bacteria
f. GM Mosquitoes - mosquito bites will spread fewer cases of serious diseases including Malaria and
Zika

Topic 2: History of Life on Earth

Geologic Time Scale (GTS) – a system of chronological dating that relates geological strata to time

Time Span
1. Age: millions of years
2. Epoch: tens of millions of years
3. Period: one hundred million years
4. Era: seven hundred million years
5. Eon: half billion years or more

● Eons: Hadean, Archean, Proterozoic, Phanerozoic

● Eras: Paleozoic (Age of Fishes); Mesozoic (Age of Reptiles); Cenozoic (Age of Mammals)
● Periods under the Paleozoic era: Cambrian, Ordovician, Silurian, Devonian, Carboniferous,
Permian
● Periods under the Mesozoic era: Triassic, Jurassic, Cretaceous
● Periods under the Cenozoic era: Tertiary and Quaternary

Fossil – preserved remains of organisms such as bones or shells of animals and leaves, seeds, or
woody parts of plants

6 Types of Fossils
1.Molds
● An impression made in a substrate
● It is the negative image of an organism
2.Casts
● When a mold such as tooth or bone is filled in
3.Petrified
● Organic material is converted into stone
● Form when minerals replace all or part of an organism
4.Original remains
● Preserved wholly (frozen in ice, trapped in tar pits, dried/ desiccated inside caves in arid regions or
encased in amber/ fossilized resin)
5.Carbon Film
● Carbon impression in sedimentary rocks
6. Ichnofossil (Trace Fossil)
● Geological record of the biological activities and behaviors of an organism

Extinction – the process by which species cease to exist

Mass extinction - The extinction of a large number of species within a relatively short period
geological time
Increased extinction rate by human activity – due to overharvesting or habitat destruction

5 Major Mass Extinction

1. Ordovician- Silurian
2. Late Devonian
3. Permian – known as the worst extinction event ever
4. Triassic- Jurassic
5. Cretaceous- Tertiary

Topic 3: Mechanisms and Patterns of Evolution

Evolution – the gradual process that occurs when genetic composition of a population changes over
successive generations; the genetic change in a population through multiple generations; it (at the
population level) refers to changes in the frequencies of genes in the population over time.
● If all organisms were the same, the entire population would be vulnerable to particular pathogens,
like viruses.
● All evolutionary adaptations (e.g. the origin of forelimbs) are the result of the gradual build-up of
genetic differences between organisms over geologic time
● In the evolutionary process, humans are unique, a totally new type of organism

Hardy-Weinberg Principle
● The original proportions of the genotypes in a population would remain constant from generation to
generation if certain assumptions are met.

5 Assumptions of Hardy-Weinberg Principle

1. No selection occurs
2. No mutation occurs
3. No migration/no gene flow occurs
4. Large population
5. Random mating occurs

Disturbances to the Hardy-Weinberg Principle

1. Gene flow – the physical flow of alleles in and out of the population
a. immigration – added
b. emigration – lost

2. Genetic drift – change in allele frequency due to chance event

a. genetic bottleneck – a sharp-lowering of a population’s gene pool
b. founder effect – reduces genetic variation when a few individuals from a population start a new
population having different allele frequency

3. Natural selection – survival of the fittest

4. Non-random mating – a mating system in which some individuals are more or less likely to mate
with individuals of a particular genotype
5. Mutation – a change in the DNA sequence
Evidences for Darwin's Theory of Common Descent
● There are patterns in the fossil record that suggest other species have diverged from a single
ancestor species.
● There are common stages in the early embryological development of organisms representing
several distinct vertebrate groups.
● There are biogeographic patterns in the distribution of species, for instance distinct bird species on
an island tend to resemble one another, suggesting a common ancestor.

Selection – the preferential survival/reproduction or preferential elimination

2 Types of Selection
1. Natural selection – selection is due to the fit of an organism with its environment, survival of the
fittest; it depends upon the fitness (the measure of an organism's adaptability to various habitats) of
the organism
2. Artificial selection – selection is due to human intervention, the breeder will select which
organisms will breed

Speciation – the process by which new species originate

1. sympatric – reproductive isolation
2. allopatric – geographical isolation
3. parapatric – groups that evolved to be separate species are geographic neighbors

Topic 4: Theories and Evidences of Evolution

Theories of Evolution
1. Lamarkism – species underwent changes in response to the changes in the environment
2. Darwinism – survival of the fittest
3. Modern Synthesis/Neo-Darwinism – recognizes other mechanisms of evolution aside from the
survival of the fittest

Evidences of Evolution
1. Paleontology – the study of fossils
● Radioactive isotopes are being used in absolute dating: potassium-argon dating, carbon dating
● Distinguishing the ancestral state of a particular species by locating a specimen of a more distantly
related species to see if it has the same characteristic

Early Hominids
1. Australopithecus afarensis – Southern ape from afar region
2. Homo habilis – Handy man
3. Homo erectus – Upright man
4. Homo neanderthalensis – Wise person from the Neander Valley
5. Homo sapiens – Modern human

2. Geographical location – closely related animals and plants were separated when the continents
slowly drifted apart millions of years ago
Examples:
a. Llamas in South America and camels in North Africa and Asia
b. Tigers and rhinos in Sumatra came from Asia
c. Cockatoos and tree kangaroos in Sulawesi came from Australia

3. Comparative Anatomy – the study of biological structures in different organisms

A. Homologous structure – same structure, different function

Example: Pentadactyl limbs in mammals

B. Analogous structure – same function, different structure

Example : Wings of bat and butterfly

Vestigial structures – diminished in size due to no apparent usage

Examples:
a. Vampire Bat – molar teeth
b. Human – appendix, wisdom tooth, ear-wiggling muscles
c. Whale – pelvic bones

4. Comparative Embryology – early development of most vertebrates are alike

5. Biochemistry – comparing the biochemistry of organisms
6. DNA homology – suggests that similar organisms have similar origins

Biochemistry and DNA homology provide the most striking evidences for evolutionary relatedness
between 2 species

Topic 5: Taxonomy and Systematics

Systematics – the scientific study of the diversity of organisms and their evolutionary relationships
Taxonomy – a component of systematics focusing on the theory and practice of classifying and
naming of organisms
Classification – involves arranging organisms into groups based on their similarities

Carolus Linnaeus – the Father of Taxonomy

2 Important Contributions
1. Hierarchical System of Classification/ Linnean System of Classification

The 5 Kingdoms:
1. Animals (all multicellular animals)
2. Plants (all green plants)
3. Fungi (molds, mushrooms, yeast)
4. Prokaryotes (bacteria, blue-green algae)
5. Protista (single-cell eukaryotes, e.g. Amoeba)

Organisms can then be ranked according to:

Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

2. Binomial nomenclature – naming of organisms using genus and species in Latin words
Examples:
a. Homo sapiens
b. Papio annubis and Papio cynocephalus which means that they belong in the same genus

● The first letter of the genus name should be capitalized while the species name should be in
lowercase

2 Types of Classification System

1. Artificial classification system – based on superficial similarities
a. Pliny the Elder (23-79 A.D.) classified animals on the basis of habits
b. Bentham and Hooker System of Classification

2. Natural classification system – based on natural affinities among the organisms and reflects the
evolutionary relationships of organisms
a. Phenetic – based on overall similarities, usually in morphology and other observable traits
b. Phylogenetic – based on evolutionary relationships between organisms

Monophyletic – share a common ancestor

Monophyletic group – includes the ancestor and all its descendants
Evolutionary classification – the grouping of organisms based on their common descent

Dichotomous Key
● It is for the classification of organism using contrasting characteristics to divide the organisms in
the key into smaller and smaller groups

Cladogram
● A branching tree-like diagram used to illustrate evolutionary (phylogenetic) relationships among
organisms.
● The basis in constructing cladogram is the shared characteristics
● Each line represents a lineage
● Each node or point of divergence branching into 2 lineages/descendance called sister groups,
indicating evolutionary divergence from a common ancestor
● The organisms which have a more recent common ancestor in a cladogram are more related to
each other.

Example of Cladogram Analysis:

Based on the cladogram above:

● Having jaws separate a tuna from a lamprey
● Amniotic egg separates a turtle from a salamander
● Turtles are the most related species to leopards
● Lancelets are the least related species to leopards

Phylogeny
● The evolutionary history of a species or group of species
● Character - a quantifiable, heritable trait
Examples: number of segments in a backbone, the presence of wings

Clade
● Group sharing one or more derived traits
● Each species is a clade
● A hypothesis based on the available information

Cladistics – considers only derived characters for analysis

Method: when there are several possible ways a group of clades can be connected, the simplest is
probably the correct one

Parsimony Analysis – process of finding the simplest pathway