BIOL1362 Exam 2 Review Sheet

CHAPTER 17 – TRANSCRIPTION AND TRANSLATION

1. Flow of genetic information: DNA RNA  Protein via transcription and translation
- Molecular differences between DNA and RNA (single-stranded, uracil instead of
thymine, ribose sugar)
DNA RNA
Double-stranded Single-stranded
Bases: A and T – C and G Bases: A and U – C and G (U instead of T)
DNA has a Deoxyribose sugar RNA has a Ribose sugar
DNA is quite stable RNA has a very short half-life

- Template strand is the strand that RNA Polymerase reads in the 3’  5’ direction
to synthesize DNA in the 5’  3’ direction; KNOW HOW
TO TRANSCRIBE A DNA SEQUENCE INTO RNA
 Template strand is the DNA strand that RNA
Polymerase reads in the 3’5’ direction to synthesize
DNA in the 5’  3’ direction; provides a template for
ordering the sequence of complementary nucleotides
in an RNA transcript.
 Coding strand is the strand starting with a 5’;
complementary to the template strand and resembles
the transcript
 RNA polymerase reads the Template strand of the
DNA in 3’  5’ direction. Coding strand is
complementary to the template strand, coded in the 5’
to 3’ direction (3 nucleotides in a series)
 RNA polymerase binds to a DNA promoter sequence
to initiate transcription, which happens in initiation,
elongation, termination.
 Initiation: a promoter is called TATA box is
recognized and DNA is unwound, a bubble is created, and RNA
synthesis begins.
 Elongation: bubble moves along the DNA template and the transcript
is elongated.
 Termination: transcript and RNA polymerase are released and the
bubble closes.
- Coding strand is complementary to template strand and also resembles the
transcript (though the transcript has Us instead of Ts)
- RNA polymerase function; the purpose of promoter sequences/TATA box and
transcription factors; recognize a transcription bubble.
  RNA polymerase copies 1 strand of the DNA
duplex into RNA. This occurs in a transcription
bubble generated by RNA polymerase binding to the
promoter. TATA box is crucial in forming the
initiation complex in eukaryotes. Transcription factors
mediate the binding of RNA polymerase and the
initiation of transcription. Completed assembly of
transcription factors and RNA polymerase II bound to
a promoter is called a transcription initiation complex.
- RNA processing: primary transcript has
introns cut out and exons spliced together; a 5’
guanine cap and a 3’ poly-A tail are added (know
why)
 A
primary
transcript is the initial RNA
transcript from any gene prior to
processing. During RNA
processing, both ends of the
primary transcript are altered.
Some interior parts of the
molecule are cut out and the other
parts spliced together.
 RNA splicing removes introns (stretches of nucleotide) and joins exons (amino
acid sequences), creating an mRNA molecule with a continuous coding
sequence.
 Both ends of the primary transcript are altered. 5’ end receives a modified GTP
nucleotide (guanine cap) 3’ end gets a poly-A tail. These modifications have
several functions facilitating the export of MRNA to the cytoplasm, protecting
MRNA from hydrolytic enzymes.
 Principles of Transcription and Translation:
1) In prokaryotes, translation of mRNA can begin before transcription has
finished
2) In eukaryotes, the nuclear envelope separates transcription from
translation
3) Eukaryotic mRNA /must be transported out of the nucleus to be
translated

2. Translation – be able to explain how it works, the steps, the components involved
and what it results in.
 Translation is when a cell reads a genetic message (mRNA) and builds a
protein. The message is a series of codons (3 nucleotides each) along with an
mRNA molecule. tRNA read the codons in mRNA and bring correct amino
acids to the ribosome, which builds the polypeptide.
 Accurate translation requires 2 steps: a correct match between a tRNA and an
amino acid, done by aminoacyl-tRNA synthetase. Then a correct match
 between the TRNA anticodon and an MRNA codon.
- The cell reads a genetic message (mRNA reading frame) and builds a polypeptide
accordingly.
- Transfer RNAs (tRNAs); how they are made (aminoacyl-tRNA sythetases)
 Anticodon in the tRNA is complementary to codons in the mRNA sequence;
tRNAs carry specific amino acids.
 tRNA molecule consists of a single RNA strand (80 nucleotides). Each tRNA can
translate a mRNA codon into a given amino acid. tRNA contains an amino acid at
1 end and other end has nucleotide triplet (anticodon) that can base pair with the
complementary codon on mRNA.
 In three dimensions, tRNA is roughly L-shaped, where one end of the L contains
the anticodon that base-pairs with an mRNA codon
- Genetic code:
 Know how many amino acids (20), how many
different codons (64), and how are codons read
(non-overlapping, 3-nucleotide words indicating
specific amino acids); though multiple codons = the
same amino acid (code is redundant for the sake of
mutations); no codon = more than 1 amino acid
- Know how to TRANSLATE mRNA INTO PROTEIN
BY READING THE CODON TABLE
- Know ribosome parts and function; P, A, and E sites
and what happens at each site (initiation, elongation,
termination)
 Charged (with amino acid) tRNA enters the A site,
the growing polypeptide is added to the amino acid
of the new tRNA, that tRNA moves to the P site,
while the naked/used tRNA moves to the E site and
then out of the ribosome; a release factor frees a
completed polypeptide by adding a water molecule
instead of another tRNA when a stop codon is
detected.
 In a ribosome, there are 3 binding sites for tRNA. P
site holds the tRNA that carries the growing
polypeptide chain. A site holds the tRNA that carries
the next amino acid to be added to the chain. E site
is the exit site where discharged tRNA’s leave the
ribosome.
  Initiation stage of translation brings
together mRNA, a tRNA with the first
amino acid, and 2 ribosomal subunits. A
small ribosomal subunit binds with
mRNA and a special initiator tRNA.
Then the small subunit along the
mRNA until it reaches the start codon
(AUG).

 In elongation, amino acids are added 1

by1 to the previous amino acid at the C-
terminus of the growing chain. Each
addition involves proteins called
elongation factors and occurs in 3
stems, codon recognition, peptide bond
formation, and translocation. (CR,
PBF, T).
 Termination occurs when a stop codon
in the mRNA reaches the A site of the
ribosome. The A site accepts a protein
called a release factor. The release
factor causes the addition of water instead of an amino acid. This reaction releases
the polypeptide, and the translation assembly then comes apart.
 Translation initiation begins
when an initiator tRNA
(Methionine) recognizes an
AUG start codon by its
anticodon and the small
subunit of a ribosome binds to
the mRNA. Then the large
subunit binds and translation
can commence.
 Start codon is AUG (methionine, M); stop (amber) codons are UAA, UAG,
UGA

3. Mutations
 Mutations are changes in the genetic material of a cell or virus.
 Point mutations are chemical changes in just 1 or a few nucleotide pairs of a gene.
- Point mutations: silent, missense, nonsense and what happens to the amino acid in
each case; be able to recognize the types using a given sequence and the amino acid
table
 A nucleotide-pair substitution replaces one nucleotide and its partner with
another pair of nucleotides
 Silent mutations have no effect on the amino acid produced by a codon
because of redundancy in the genetic code.
 Missense mutations still code for an amino acid, but not the correct amino
 acid (substitution mutations are usually missense mutations). A different
protein would be produced.
 Nonsense mutations change an amino acid codon into a stop codon,
nearly always leading to a nonfunctional protein.
 Nucleotide-pair deletion: frameshift causing extensive missense.

- Insertion and deletion of nucleotides/codon and how it affects the reading frame of
the mRNA and translation into protein
 Insertions and deletions are additions or losses of nucleotide pairs in a gene; may
alter the reading frame of the genetic message, producing a frameshift mutation.
 These mutations have a disastrous effect on the resulting protein more often than
substitutions do
CHAPTER 19 – REGULATION OF EUKARYOTIC GENE EXPRESSION
1. Regulation of eukaryotic gene expression
 All organisms regulate which genes are expressed at any given time.
 Almost all the cells in an organism are genetically identical
 Regulation of gene expression is essential for cell specialization.
 Differences between cell types result from differential gene expression (the
expression of different genes by cells with the same genome).
 Abnormalities in gene expression can lead to diseases, including cancer
- Histone tail modification: can loosen or condense chromatin, can activate or
repress gene expression
 Histone acetylation, acetyl groups are attached to positively charged lysine
in histone tails. This generally loosens chromatin structure, promoting the
initiation of transcription.
- DNA Methylation (epigenetics): reversible DNA modifications that activate or
repress gene expression and can be inherited.
 Addition of methyl groups (methylation) can condense chromatin and lead
to reduced transcription. Methylation usually happens with the base
cytosine. Inheritance of trains transmitted by mechanisms not directly
involving the nucleotide sequence is called epigenetic inheritance
Epigenetic modifications can be reversed, unlike mutations in DNA.
- RNA Polymerase needs transcription factors: general transcription
factors or (low-level expression) and specific transcription factors.
 Starting transcription, eukaryotic RNA polymerase requires the
assistance of proteins called transcription factors. General
transcription factors are essential for the transcription by RNA
polymerase II, but are usually only capable of low level transcription.
In eukaryotes, high levels of transcription of particular genes depend
on interaction between control elements and specific transcription
factors.
- Control elements: DNA sequences binding sites for transcription factors that assist with
gene expression; proximal elements – close to promoter; enhancer elements – can be
near or far and few or many
 Control elements: segments of noncoding DNA that serve as binding sites for
transcription factors that help regulate transcription. Control elements and the
transcription factors they find are critical for the precise regulation of gene
expression in different cell types.
 Proximal control elements close to promoter
 Enhancer elements: thousands of nucleotides up- or downstream; genes can
have multiple enhancers; gene expression increased or decreased. Activators or
repressors can bind to control elements of enhancers.

- Activators: proteins like transcription factors that bind enhancer DNA elements to
increase expression.
- Repressors: proteins that bind silencer DNA sequences to decrease expression,
can bind to control elements to influence gene expression
- Know the differences between eukaryotic and prokaryotic gene expression
control; e.g. bacteria have promoters and RNA polymerase, but do not
have enhancer sequences, whereas eukaryotes do.
 Prokaryotes: require regulatory proteins. In PROKARYOTES, activator
and repressor proteins act on operators (DNA sequences just downstream
of the promoter). They do not have enhancer sequences.
 Eukaryotes: activator proteins act on enhancer sequences; repressor
proteins act on silencer DNA sequences. Enhancers can be found either
 upstream or downstream of the promoter. Position of the enhancer has a
profound effect on gene regulation.
- Study the teamwork exercise on regulatory elements (example: enhancers)

CHAPTER 21 – GENE EXPRESSION & DEVELOPMENT

1. Genes like “master regulatory genes” regulate other genes by induction
- Differentiation and morphogenesis; differential gene expression;
programmed cell death/apoptosis.
 Signals that are produced by cells influence their neighbors to
divide, differentiate, move, expand, or die is
what induction does.
 Cell differentiation is the process by which
cells become specialized in structure and
function.
 Programmed cell death is a highly regulated
and essential part of development; occurs in
both plants and animals, helps tissues and
organs take shape
 Apoptosis is the most common type in
animals. Examples include cells that form
webbing between toes die, about ½ of neurons
die as nervous system is wired, harmful
immune cells are eliminated.
- Drosophila life cycle
- Pattern formation in fruit fly; positional information;
know the major axes.
 Pattern formation is the development of a spatial
organization of tissues and organs.
 Positional information are the molecular cues that
control pattern formation, tells a cell its location
relative to the body axes and to neighboring cells.
 Anterior is towards the head. ventral is the front.
Dorsal is towards the back. Posterior is towards the
tail.
- Nusselhein-Volhard/Weischaus mutant screen identified genes controlling
developmental patterning; know what maternal effect genes do and what
happens to the embryo if maternal effect genes are mutated; problems with
deposition of maternal effect mRNA in an egg will affect all offspring equally;
know what bicoid does.
 Maternal effect genes encode cytoplasmic determinants that initially
establish the axes of the body of Drosophila. Maternal effect genes aka egg-
polarity genes, because they control orientation of the egg and consequently
the fly.
 Bicoid a maternal effect gene affects the front half of the body. An embryo
whose mother has no functional bicoid gene lacks the front half of its body
and has duplicate posterior structures at both ends.
- Know what morphogens are and how researchers figured out that bicoid was
expressed as a morphogen, where it was found in the embryo, and what type of
protein it is.
 A morphogen is a molecule that emanates from a specific set of cells that is
present in a concentration gradient and that specifies the fate of each cell
along this gradient.
 First, they obtain a single-stranded DNA or RNA complementary in
sequence to target mRNA. Then they add fluorescent label to the probe.
Copies of probe were added to preserved cells made permeable to probe. The
probe then binds to complementary target mRNA. Then they can observe the
location of probe by microscopy.
 Bicoid mRNA was distributed in a gradient in Drosophila embryos. Highest
concentration was at the anterior end. Bicoid mRNA is made by cells of the
mother and transferred into the egg
- Understand what homeotic genes are (determine organ formation);
homeobox genes are examples of homeotic genes; recognize hox gene
organization, evolutionary conservation (which organisms have Hox genes)
and the consequences of altering expression of homoebox genes (phenotypes
like Antennapedia and bithorax in the fruitfly).
 Lewis discovered the homeobox (Hox) genes: master control (homeotic)
genes that initiate pattern formation (organ development in specific parts
of the body) in late embryo, larva, and adult stages.
 Homeosis is the transformation of one organ into another via mutation.
Homeosis is caused by mutations in Hox genes. These mutations lead to
transformations in the identity of entire body parts.
 Hox genes guide pattern formation in embryos - tell the cells of the body
how to differentiate as the body grows. They also reveal the shared
evolutionary history of life.
 Hox genes occur in groups such as prokaryotes, yeast, plants, and animals
 Hox proteins are transcription
factors that regulate many other
genes.
 Drosophila Hox genes are
found in clusters (corresponds
to the order of where the genes
are expressed in the embryo).
Almost all animals contain
related sets of Hox genes.
 If developmental processes are disrupted, the embryo is likely to die. If a
process is modified, it may lead to changes in size, shape, or activity of a
structure.
 Evolutionary developmental biology, or evo-devo, focuses on
understanding:
1) How changes in developmentally important genes
2) Led to evolution of new forms.
 - Be able to explain how gaining or losing developmental patterning
genes can lead to gain or loss of certain structures (example: loss of
Hox6/8 overlapping expression results in loss of forelimbs, while loss
of Sonic hedgehog could result in loss of hindlimbs)
 Hoxc6 and Hoxc8 are both expressed in cells where ribs form. Only
Hoxc6 is expressed in the region where forelimbs form.
 Hoxc6 and Hoxc8 are both
expressed in snake embryos.
 A change in regulation of
where Hoxc8 is expressed
led to the loss of the
forelimb. Snakes make ribs
instead of forelimbs
 Hindlimb loss in snakes is
due to failure to produce the
signaling molecule sonic
hedgehog.
 Loss of sonic hedgehog signaling in the pelvic region of whales led
to the disappearance of their Hindlimb

CHAPTER 22 – DARWIN AND NATURAL SELECTION

1. Charles Darwin
- Where did Darwin journey to and what did he observe
 Darwin went to the Galapagos from April to October 1835, located approximately
1000km from the coast of Ecuador, South America. The islands is a natural
laboratory where evolution can be observed.
 Adaptation to the environment related to the origin of new species; also, he
observed that though many species have difference to each other and the fossil
record, there is also striking relatedness and he concluded that all organisms must
somehow be related by a common ancestor; he drew something like a family tree
or the first phylogeny
- Evolution was not a new idea
 Evolution is genetic change through time. Natural selection a mechanism of
evolution. It requires heritable variation, differential survival and reproduction.
Natural environment of an organism “selects” for traits that confer a reproductive
advantage, causing gradual changes or evolution of populations or species.
 Evolution by natural selection can be observed within short periods of time. It is
advantageous to have different traits as the selective environment changes.
- Darwin (with Alfred Russell Wallace) proposed:
 Natural selection is the mechanism behind the evolution of species in nature
(versus artificial selection caused by humans); the traits of some organisms make
them better suited to their environment, more able to survive and reproduce than
other organisms and pass on their genetic material to the next generation.

2. Darwin’s Finches and Natural Selection Case Study

- Endemic species on the Galapagos islands
  Animals that live there that are found nowhere else on earth. This makes them
endemic. Endemics include 1 penguin species, 1 giant tortoise, 1 marina iguana,
7 species of lava lizard, 14 species of sea cucumber, 1 sea lion, 1 hawk, several
species each of mockingbirds, doves, owls, flycatchers, and yellow warblers.
- Peter and Rosemary Grant’s research on Galapagos finches
 Peter and Rosemary Grant have studied many of these species for the past thirty
years.
 Finches feed on seeds
 Finches with small beaks generally eat smaller seeds
 Finches with large beaks can eat small and large seeds
 A variety of seeds are produced on the island but finches prefer the
softest seeds which are easiest to open
- What occurred on the island from 1976-1978 and what resulted in the finch
populations?
 Studied changes in beak depth as a result of changing weather over 3 years:
 In a normal year, 130mm of rain would fall on the islands. In 1976 (year
1), 137 mm of rain fell. In 1977 (year 2), total rainfall for the year 24mm.
In 1978 (year 3), more than 50mm of rain fell on the island. Finch
population went down. No finches birthed in 1977. Only 1 finch born in
1977 survived to 1978. Finches have different beaks for different diets.
 Order of events: weather change  well-adapted (physiological traits) animals
leave more offspring  gene frequencies in the population change
 Evolution by natural selection:
1) Individuals vary in some traits
2) Some of the differences in traits are passed along to offspring. (requires
a genetic basis to the trait, trait is thus heritable)
3) Different individuals produce different # of surviving offspring (produce
different numbers or different numbers survive.
4) Particular value of a trait is connected to # of offspring produced (traits
that allow for more offspring to be produced are said to be “naturally
selected”
 Evolution can be observed within a short period of time and is reversible.
Evolution can occur at very small scales.
 Natural selection does not happen to individuals, but within populations Individual
organisms do not change to adapt or evolve during their lifetimes; some organisms
have genes have already provided them with certain phenotypes that make them
more adaptable to their environment, which allows them to leave more offspring
than less adapted individuals
 Evolution by natural selection cannot occur without heritability; evolution is
genetic change through time

CHAPTER 23 – POPULATION EVOLUTION

1. Microevolution, be able to explain the mechanism of evolution by natural selection
 Microevolution: change in allele frequencies in a population over generation.
 Natural Selection: the only mechanism causing adaptive evolution (improving the
match between organisms and their environment)
  Genetic drift: chance events altering survival and reproduction, and thus allele
frequency; tends to reduce genetic variation through losses of alleles, especially in
small populations
 Founder effect: a few individuals become isolated from a larger population;
allele frequencies may not represent the larger population
 Bottleneck effect: a drastic reduction in population (as in a sudden
environmental change) results in a gene pool that no longer reflections the
population’s gene pool. If the population recovers, it may not be very
genetically diverse. Significant in small populations; disproportionately-
represented alleles; can cause allele frequencies to change at random; leads to
loss of genetic variation; influences adaptation to an environment; can cause
harmful alleles to become fixed; threatens survival.
 Gene flow: transfer of alleles between populations; can increase (example:
mosquito resistance spreading) or decrease the fitness of a population; movement
through individuals and/or gametes
 Ex: Mosquitoes’ alleles over time have evolved to where they are resistant
to insecticides, therefore increasing the fitness.
- Requires variation in heritable traits to be present in a population; understand the
types of genetic variation (mutations and such); natural selection can only act on
phenotypic variation that has a genetic component
 Variation in heritable traits is a prerequisite for evolution. Phenotypic variation
often reflects genetic variation. Without genetic variation, evolution cannot occur.
 Sources of genetic variation include mutation or gene duplication. Only mutations
in gametes can be passed to offspring. Effects of point mutations can vary:
 Mutations in noncoding regions of DNA are often harmless
 Mutations to genes can be neutral because of redundancy in the genetic code
 Mutations that alter the phenotype are often harmful
 Mutations that result in a change in protein production can sometimes be
beneficial.
 Duplicated genes can take on new functions by further mutation
 Ancestral odor-detecting gene has been duplicated many times: humans
have 350 functional copies of the gene; mice have 1,000.

2. Populations and gene pool definition

- Hardy-Weinberg principle – counting allele frequencies and genotype
frequencies to determine if a population is evolving
- If a population meets Hardy-Weinberg criteria, it is not evolving
- Know how to calculate the number and frequencies of alleles in a population; sum
of 2 alleles for one genetic locus (example A and a in a population) is p + q = 1;
remember to count both dominant and recessive alleles in both homozygous (AA
and aa) and heterozygous individuals (aa) when considering allele frequencies.
 - p2 + 2pq + q2 = 1; know how to calculate genotype frequency (AA = p x p; Aa = 2
x p x q; and aa = q x q) in a
population given p or q.
- Five conditions for populations
to be non-evolving (if any of these
things occurs, the population can
evolve – even at individual genes)
1) No mutation
2) Random mating
3) No natural selection
4) Very large population size
5) No gene flow

3. Selective mechanisms
- Phenotypes come in variety, often
a continuous spectrum. Not every
 Directional selection: favors individuals at one end of a phenotypic range
 Disruptive selection: favors individuals at both extremes of a phenotypic range
 Stabilizing selection: favors intermediate phenotypes and acts against extreme
phenotypes
- Adaptive evolution is a continuous, dynamic process for many organisms

4. Study the teamwork exercise on population genetics and phylogeny

CHAPTER 25 – MACROEVOLUTION & PHYLOGENY

1. Study the teamwork exercise on population genetics and phylogeny

2. Macroevolution:
 Macroevolution: bigger changes that happen above the level of species (ex: the
origin of mammals or radiation of plants)
 Speciation: the process by which one species splits into two or more species.
3. Phylogeny:
 The evolutionary history of a species or group of related species.
 Demonstrates the evolutionary history of a species or groups of species; show
patterns of descent, no phenotypic similarity; they do not generally indicate when
a species evolved or how much change occurred (these things have to be noted in a
tree to be considered); cannot be assumed that one taxon evolved from the taxon
next to it, just that they had a common ancestor.
- Understand taxonomy and binomial nomenclature
 Taxonomy is the ordered division and naming of organisms.
 Binomial nomenclature is a 2-part scientific name (Latin) of a species. First part of
the name is the genus. Second part, called the specific epithet, is unique for each
species within the genus. The first letter of the genus is capitalized, and the entire
species name is italicized (D. melanogaster). King Phillip came over for good
species. (kingdom, phylum, class, order, family, genus, species)
- Know how to read phylogenetic trees and consider relationships between organisms
(more or less related compared to other members of the tree)

 A phylogenetic tree represents a hypothesis about evolutionary relationships.

 Phylogenetic trees show patterns of descent, not phenotypic similarities.
 Phylogenetic trees do not generally indicate when a species evolved or how
much change occurred in a lineage.
 It should not be assumed that a taxon evolved from the taxon next to it.
- Key vocab words: taxa/taxon, branch point, clade, basal taxon, sister taxa, outgroup
 A taxonomic unit at any level of hierarchy is called a taxon.
 A rooted tree includes a branch to represent the most recent common ancestor of
all taxa in the tree.
 A basal taxon diverged early in the history of a group and originates near the
common ancestor of the group.
 Sister taxa are groups that are an immediate common ancestor.
 A clade is a group of species
that includes an ancestral species
and all its descendants.
 An outgroup is a species or
group of species that is closely
related to the ingroup, the
various species being studied.
 Each branch point represents
the divergence of two taxa from
a common ancestor.
 A polytomy is a branch from
which more than two groups
emerge
- Be able to describe homology (similar due to shared ancestry) vs. analogy (similar
due to convergent evolution; similar environments caused unrelated species to
develop similar adaptive traits)
 Phenotypic and genetic similarities due to shared ancestry are called homologies.
 Analogy is similarity due to convergent evolution. Convergent evolution occurs
when similar environmental pressures and natural selection produce similar
 (analogous) adaptations in organism from different evolutionary lineages.
 Homoplasy are analogous structures or molecular sequences that evolved
independently (ex: bat and bird wings are homologous as forelimbs but
analogous as functional wings.)
 Molecular homologies are based on similarity at the DNA (or protein) level;
phylogenetic trees based on DNA sequences changes: length of a branch can reflect
number of genetic changes.
 Shared ancestral characters: originated in an ancestor of a taxon
 Shared derived characters: evolutionary novelty that is unique to a clade or taxon
 Some characters can be both ancestral and derived depending on context
Narrow possibilities by applying the principle of maximum parsimony: the tree that
requires the fewest evolutionary events (appearances of shared derived characters) is the
most likely.