Biology Second Semester Study Guide
Molecular Genetics (Chapter 10)
DNA = Deoxyribonucleic Acid DNA is the blueprint for who we are and for who we have become
STRUCTURE
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The structure of DNA, its double helix shape, was discovered by Watson and Crick.
DNA is a nucleic acid (polymer) made from nucleotides (the monomers of nucleic acids).
Each nucleotide is made of a phosphate, a sugar, and a base. The base is bonded to the sugar which is
bonded to phosphates. The sugars and phosphates bond together (phosphodiester bond) in an alternating
pattern the forms the backbone of DNA.
The nucleotides of DNA contain 4 bases, the purines (double-rings) are Adenine and Guanine and the
pyrimidines (single-rings) are Cytosine and Thymine. These nucleotides combine to form a strand of
DNA.
DNA is a double stranded molecule. The strands are held together by hydrogen bonds between the bases.
Adenine bonds with Thymine and is held by two hydrogen bonds, and Cytosine bonds with Guanine and is
held together by three hydrogen bonds. It is this difference in bond number and thus strength that accounts
for the helical shape.
Due to the phosphates in the DNA strand a DNA molecule of DNA has a slightly negative charge.
Chromosome Composition Chromosomes are made up of DNA and protein. The DNA is coiled around the
proteins (histones) and then folded over itself.
DNA Replication DNA replication is semi-conservative. This means that each new DNA molecule has half of the
original. In order to begin replication, DNA is unwound (unzipped) by DNA helicase. Helix-destabilizing proteins
keep the helix in the unzipped position until the complimentary bases are added. DNA Polymerase catalyzes the
linking together of nucleotide subunits in a 5' to 3' direction as always.
Transcription:
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This is where the DNA
code is copied (transcribed)
into mRNA codon
language.
In a general sense,
transcription is the process
of copying the specific
needed recipe from the
huge cookbook, trimming
off all the excess and sending out to be made.
happens within the nucleus, then the mRNA travels to the
cytoplasm.
DNA base triplet code (gene) must be copied into
complementary mRNA codons (A,U,C,G)
Translation
 Occurs in the cytoplasm/ribosomes
 This is where tRNA anticodons match up with the complementary mRNA
codons
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Biology Second Semester Study Guide
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tRNA delivers the correct amino acids to the ribosomes., so the protein can be assembled
At the ribosome, protein synthesis consists of: INITIATION (start code), ELONGATION(adding amino
acids to chain), TERMINATION(stop code).
Additional skills:
 Know how to complement DNA. If a DNA strand has a code of TACCTTGGGACGATC, what would its
complementary strand read?
 You should also be able to “decode” the strand into amino acids, using a base triplet decode key.
 Transcription: you should also be able to write the complementary mRNA code that would match up with
the DNA code given.
CELL DIVISION (Chapter 8)
Mitosis: Purpose? Stages? Example: what stage is this 
Purpose - growth and repair; allows for direct replication of a cell
INTERPHASE
G1 (longest phase), rapid growth of organelles
Synthesis - DNA replication
G2- growth continues, final preparation for mitosis, spindles form
MITOSIS - (shortest phase), Prophase, Metaphase, Anaphase, Telophase
Cytokinesis, occurs, then leads back to >>>>>>>> INTERPHASE
Meiosis: Purpose? Stages?
Purpose - reproduction; allows for the formation of haploid gamete cells
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Germ cells of eukaryotes produce gametes
2 Divisions ending in 4 cells that are different from each other and parents
Stages
INTERPHASE -chromosomes replicated in the S-phase
PROPHASE I -nucleus and nuclear membrane break down; centrioles move towards opposite poles; tetrads
formed
METAPHASE I -homologous pair line up along equator
ANAPHASE I -homologues separate and move to opposite poles
TELOPHASE I -chromosomes at opposite poles; new cell membranes form through cytokinesis
PROPHASE II
METAPHASE II
ANAPHASE II
TELOPHASE II
Variation There are several ways that Meiosis produces variation in organisms.
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When homologous chromosomes meet at the equator to form a tetrad, crossing over can sometimes occur
among sister chromatids.
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Biology Second Semester Study Guide
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In crossing over, the genes switch places on homologous chromosomes and travel with their new
chromosomes through the remained of the process of meiosis. This increases variation in the gametes, and
thus offspring.
Independent Assortment refers to the quality that chromosomes will sort into different cells during meiosis
independent of one another.
Both crossing over and independent assortment increase genetic variation in reproduction of a species,
allowing for evolution. Species which reproduce by mitosis have less genetic variation, which can only be
achieved through mutations.
Genetics and Inheritance (Chapters 9, 11, 12)
Terms:
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Mendelian principles
gene
locus
allele
dominant
recessive
homozygous
heterozygous
genotype
phenotype
Phenotypic ratio
Punnett Square
autosome
sex chromosome
seX-linked inheritance
polygenic inheritance
incomplete dominance
codominance
Down's syndrome (trisomy)
Klinefelter's syndrome
Turner's syndrome
deletion
duplication
translocation
sickle cell disease
nondisjunction
karyotype
Variation There are several ways that Meiosis produces variation in organisms.
Crossing Over - When a tetrad forms, the tips of the homologous chromosomes can switch, allowing for random
variation during Prophase I.
Mutations - Random genetic accidents can mutate genes.
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Insertion - DNA put in
Deletion - DNA taken out
Inversion - DNA reversed
Translocation - DNA cut out somewhere and stuck back in somewhere else
Independent Assortment - Chromosomes line up independently during meiosis, creating a near infinite amount of
combinations.
Linked Genes are located on the same chromosome and are inherited together. They do not assort independently. Linked
genes will only form recombinants if crossing over has occurred
Genetic Recombination: production of offspring with different traits than the parents
Genetic terminology:
Genotype-alleles on a homologous chromosome that show the characteristics of the trait that the homologous chromosome
codes for
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Biology Second Semester Study Guide
Phenotype- The observable physical characteristics determined by genes
Locus-The position of a gene on a chromosome
Homozygous- two identical alleles of a gene [ gene with two identical alleles, either dominant of recessive (ex. HH or
hh)]
Heterozygous- two different alleles of a gene [one dominant allele and one recessive allele (ex. Hh0]
Dominant Allele- an allele that is dominant in regards to the phenotype whether it is part of a homozygous or
heterozygous combination
Recessive Allele- An allele that does not show if a dominant allele is present, but shows when an organism has a trait
that is homozygous recessive
Test Cross-Testing for a heterozygote by crossing it with a known homozygous recessive organism
Punnett Squares: practice! Try to find F1 offspring % predictions for:
(a) HH x hh; (b) Hh x Hh; (c) Hh x hh combos. Phenotypes? Genotypes?
What about incomplete dominance? Roan x roan cattle, for instance (RW x RW). What color offspring would you
predict?
Carrier- An organism that has a recessive allele of a gene that does not effect it, but that it may pass down to its
offspring
Codominant Alleles-Pairs of alleles that equally affect the phenotype even though they are
heterozygote
P Generation: Parent Generation
F1 Generation: The offspring of the parent generation
F2 Generation: The offspring of the F1 Generation
Multiple alleles-three or more alleles of a single locus. ex.blood types
Sometimes when traits are crossed people end up getting traits that are known as Hybrid
Vigor. This is when superiority arises from the heterozygote as oppose to homozygous genotypes. Some examples of hybrid
vigors are mules, and Sickle cell when it is a heterozygote because the people cannot get malaria, but they can still carry
oxygen.
Know how to read a pedigree
Mutation- a change on the chromosome or in the gene that gives the offspring different DNA/
traits from the parents.
Diploid: having the full set of chromosomes (2n or 46 chromosomes)
Haploid: gametes (egg and sperm) only half the number of chromosomes (n)
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Biology Second Semester Study Guide
Polyploid- refers to the possession of more than one set of chromosomes. [Polyploid organisms, especially plants, are
larger than normal and have larger cells. Affected animals are often abnormal in appearance and usually infertile.]
Polygenic Inheritance: Polygenic inheritance refers to traits that are determined by more than one gene. For instance,
skin color, hair color, or eye color. There isn't just black or blonde hair, but varying shades of each due to polygenic
inheritance.
Sex-linked Traits: A sex-linked trait is due to a gene found only on the X chromosome, otherwise known as the sex
chromosome. One example is colorblindness, which males are more likely to get because they have two X chromosomes
to a female's one, thus, in effect, doubling their chances of being affected.
Karyotype: A karyotype is a picture (photomicrograph ) of the chromosome composition of an individual (generally
numbered in order of size). Karyotypes are used to identify certain genetic disorders. For example, if the karyotype
reveals trisomy on chromosome 21 then the person has Down syndrome.
Linkage Group: Genes in a particular chromosome that tend to be inherited together.
Mathematics & Genetics
Probability - The fraction, percentage, or ratio that is used to describe the chance of an event occurring. In genetics,
probabilities predict phenotypes and genotypes that come from genetic crosses.
Product Rule - The probability that two or more independent events will occur together is found using the product of the
individual probabilities of each event. If the probability of a cross between a tall pea plant and a short pea plant
producing a short pea plant is 25%, what is the probability of three short plants being produced in a row? The answer can
be found using the product rule: 0.25x0.25x0.25=0.015625 or 1/64. So there is a 1 in 64 chance that three short plants
will be produced in a row.
Hardy-Weinberg principle - Named after English mathematician Godfrey Hardy and German physician Wilhelm
Weinberg, this principle shows the expected frequencies of different genotypes in a population. Though this rule
represents an ideal population in which there is:
 random mating,
 no mutation,
 a large population size,
 no migration (emigration or immigration) and
 no natural selection
EVOLUTION (Chapters 14, 15, 16)
Probable Origins of Life:
How old is the Earth? Based on what evidence/data?
What evidence do we have of the first living things? How old? What were they like?
Possible origin of life on earth?
Alexander Oparin’s Hypothesis
The MILLER AND UREY experiment: They conducted an experiment which would change the approach of scientific
investigation into the origin of life. Miller took molecules which were believed to represent the major components of the
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Biology Second Semester Study Guide
early Earth's atmosphere (Water, Hydrogen, Ammonia, and Methane (WHAM)) and put them into a closed system. The gases
they used were methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O). Next, he ran a continuous electric current
through the system, to simulate lightning storms believed to be common on the early earth. Two percent of the carbon had
formed some of the amino acids which are used to make proteins. Perhaps most importantly, Miller's experiment showed that
organic compounds such as amino acids, which are essential to cellular life, could be made easily under the conditions that
scientists believed to be present on the early earth. This enormous finding inspired a multitude of further experiments.
Other Theories of how we got here
Cosmic Origins of first organic molecules (building blocks of 1 st cells). Also called “Exogenesis” (cosmic origins), but
more commonly known as panspermia. The actual theory of panspermia speculates that life came to earth from another
planet, perhaps being carried by a meteorite that crashed here. This theory solves the time gap that we currently have in our
evolution chart, and several meteorites have been recovered by scientists that HAVE organic matter in them.
Other than life originating chemically on earth (Miller-Urey, Oparin) or from extraterrestrial origins, another theory that is
used to explain evolution is creationism (Intelligent Design). This describes how God created the Earth and everything that
surrounds it. This implies some higher being created everything on Earth and is guiding them through their existence.
Origins of Eukaryotic Cells: Endosymbiosis is the theory proposed by Lynn Margulis which suggests that eukaryotic cells
evolved from prokaryotic cells. Basically endosymbiosis states that a prokaryotic cell consumed other prokaryotic cells, in
this case mitochondria and chloroplasts. They grew to have a symbiotic relationship and eventually went on live together in
peace. The reason this is believed to be true is because mitochondria and chloroplasts have their own DNA.
Darwin-Wallace Theory of Natural Selection
Evolution is based on four observations about the natural world:
1. Overproduction: each species produces more offspring than will survive
2. Variation: individuals in a population exhibit variation
3. Limits on population growth: environmental factors limit growth, causing a struggle for existence
4. Differential reproductive success: those with the most favorable characteristics are more likely to survive and
reproduce
Natural Selection
Natural Selection is the principle that nature tends to favor organisms with certain traits. These organisms therefore have a
greater chance of survival in that environment than other organisms without the trait. This gives the organisms with the trait a
significant advantage in the environment. Because it has a greater chance of survival, and organism with the trait is less likely
to die young and has a greater chance of reproducing early and often to spread its genes. It then can pass on this beneficial
trait, allowing the trait to proliferate throughout the species. In this way, natural selection favors organisms with certain traits,
giving them a greater chance to survive and pass on these traits so that more of the population can survive using this
favorable trait.
Adaptation: An evolutionary modification that causes the chances of survival and successful reproduction much higher.
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Biology Second Semester Study Guide
Modern Examples of Evolution.
Explain any one of these:
-In response to the widespread use of the pesticide, some species of insects have become immune/resistant
-Penicillin resistant strains of bacteria due to the widespread use of the antibiotic
-Some mosquitoes resistant to DDT
-Evolution of Peppered Moth due to predation and changes in environment
Evolution is the change in a populations overall traits and usually refers to the genes passed on from generation to generation.
Evolution is used to map out the growth of a population as well as the mutations that affect/ change it. Natural selection is
one way of causing a population to evolve and natural selection means that heritable traits that are more helpful to survival
are the ones most likely to be passed on from generation to generation
Before that, there was the Lamarckian theory which stated that traits acquired during a lifetime would be passed on to the
next generation.
Recombination and assortment allow for variation (and mutations) in a population. In addition, random mutations add new
material (genes) for selection.
Charles Darwin - Darwin believed that the Earth was very old and its form had transformed over a period of time. Artificial
selection supposedly could allow breeders to choose traits that they liked. Darwin used this process to explain a similar
process that occurs in nature. Some of Darwin’s influences:
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Alfred Wallace - Sent Darwin a published paper of his ideas, which were quite similar to those of Darwin himself.
Thus, the Darwin-Wallace Theory of Evolution was born; this theory held that four key aspects of life lead to
evolution: population variation, overproduction, limits on population growth, and differential reproductive success.
Thomas Malthus - Wrote An Essay on the Principle of Population as It Affects the Future Improvement of Society.
In it, he stated that growth in a population is not always desirable. Populations can increase exponentially, while the
population's food supply can only increase arithmetically. Because of this problem between food supply and
population, famine, disease and war can occur, halting population growth.
Evidence for Evolution:
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Geological Distribution of living organisms
Fossils
Radioactive Dating
Biochemical evidence: the universality of DNA and protein structures
Embryo evidence because all embryos look alike in the early stage of
Homologous structures (forelimbs of different vertebrate groups = same bone structure)
Vestigial organs (appendix, coccyx bone)
Evolution terms:
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Natural selection
Mutations (positive/negative/neutral)
phylogeny
era
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Biology Second Semester Study Guide
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period
epoch
chemical evolution
Homologous/analogous
Vestigial structures
Divergent –vs- convergent evolution
Microevolution in populations (peppered moth, Darwin’s finches)
Directional/stabilizing/disruptive selection (picture: bell curves)
Speciation – how does it happen?
Hardy-Weinberg Principle: under certain conditions, populations will stay in genetic equilibrium from generation to
generation (not evolving)
There will also be a few questions about some overarching topics that have been incorporated (including
laboratories you’ve done) throughout the entire year. Review the following…
CLASSIFICATION (Chapter 17)
Classification is pretty much the single greatest thing since sliced bread. Maybe even before sliced bread. It allows organisms
to be grouped together based on their similar characteristics. There are a lot of organisms, so this is important. This variety of
organisms (and their ecosystems!) is known as biological diversity. The study of said diversity is systematics. Classifying and
naming organisms is known as taxonomy. We use a binomial nomenclature when referring to organisms. The binomial
nomenclature was designed by Carolus Linnaeus and consists of an organism’s genus and species. Both words have Latin
roots.
WHAT'S A SPECIES? A species is a potentially interbreeding population. Remember, the offspring must also be able to
reproduce. A population is a group of the same species. A community is a group of populations, cohabitating. This habitat is
known as the ecosystem. A group of ecosystems makes up a biome (think temperate forest, or tundra!) The entire world,
and/or all the biomes and life and everything, makes up the biosphere.
Classification System: A classification system is something that helps scientists to organize animals, plants, and other life
into categories so that we can see similarities and differences.
Our modern classification system consists of:
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Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Binomial Nomenclature: This is the specific system of naming in which scientists derive names of organisms with respect
to their Genus and Species. For instance, humans are classified as Homo (genus) sapiens (species). This allows for a continuity
and common ground for naming organisms throughout science, facilitating research and building a foundation for further
study into biology.
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Biology Second Semester Study Guide
Ecology and Human Impact on the Environment (a recurring theme throughout the year)
Terms:
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Symbiosis
Mutualism
Commensalism
Parasitism
species
population
community
ecosystem
growth curve
world population
United States population
ecological community
food chain, food web
trophic levels
autotrophs
biomass
heterotrophy
producer
consumer
decomposer
herbivores
carnivores
omnivores
energy loss
biological magnification
DDT
ecosystem
biotic
abiotic
greenhouse effect
acid rain
CFCs
Greenhouse gases
Fossil fuels
soil pollution
erosion
deforestation
global warming
eutrophication
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