Study Guide: Exam 4
Chapter 15: Gene Activity
- Genes specify enzymes: the bread mold fungus was used to show that loss of a gene that encoded an enzyme in a metabolic pathway could be determined by growing the mold in the presence or absence of individual metabolites in the pathway, and finding out where in the pathway the missing enzyme functions
- Genes specify polypeptides (proteins are composed of 1 or more polypeptides)
- some genes only specify RNA molecules (tRNA and rRNA)
Gene Expression:
DNA is transcribed to RNA in the nucleus
-
primary mRNA is modified in the nucleus:
- 5ı cap and poly-A tail are added
- splicing of exons together with removal of introns
- Transcription is carried out by a 5ı to 3ı RNA Polymerase, as well as additional protein factors
- The result of these modifications is mature mRNA
Mature mRNA is translated to protein in the cytoplasm
- Translation occurs at the ribosomes
- Many ribosomes may synthesize protein from the same mRNA molecule at the same time (polyribosomes)
- tRNA molecules carry amino acids to the ribosome during translation (a tRNA for each amino acid)
- rRNA along with proteins comprise the structure of the 2 subunits of the ribosome
- Ribosome subunits associate immediately prior to translation, and dissociate following translation
- Ribosomes bind mRNA at the 5ı cap, assisted by rRNA components, and begin translation, usually, at the first AUG (start) codon
- The initiator (AUG/methionine) binds to the P site to begin translation all following tRNAs bind to the A site, and transfer their amino acids to the growing polypeptide at the P site
- Following translation, a release factor cleaves the complete polypeptide from the last tRNA and the ribosome, and the polypeptide leaves the ribosome
Mutations:
Point mutations: (Substitutions) change the identity of a single nucleotide in DNA (can lead to disorders, as is the case with sickle-cell disease)
Insertions & Deletions: addition of 1 or more nucleotides (insertion), or removal of 1 or more nucleotides (deletion) to DNA
- can lead to frame-shift mutation: at the point of insertion or deletion, every codon that follows is changed
- can introduce stop codon
- multiples of 3 bases only change 1 codon
Mutagens (ultraviolet light, chemical carcinogens (pesticides, cigarette smoke) cause mutations
- DNA repair enzymes can correct some mutations
Cloning a gene:
- Plasmids: small accessory circles of DNA (from bacteria)
- Foreign genes (or any gene of interest) can be introduced into plasmid DNA.
- Transformation: Bacteria cells take up plasmid DNA & replicate the plasmid along with their own DNA.
- Viruses can also be used to clone genes viruses that infect bacteria are called bacteriophages.
Clone: a large number of molecules, cells, or organisms that are identical to the original.
Polymerase Chain Reaction: DNA Polymerase carries out replication of a specific DNA sequence repeatedly until there are millions of copies.
- useful for cloning a specific DNA sequence from genomic DNA (all the DNA from one cell).
- uses DNA primers (small single-starnded fragments of DNA that have a sequence complementary to the regions flanking the sequence of interest.
Transgenic Organisms: organisms carrying a foreign gene in their DNA.
- Transgenic Bacteria: can produce large quantities of a favorable gene product (polypeptide) that can benefit the environment (protect plants with toxins or degrade oil in oil spills)
- Transgenic Plants: genetically favorable crops; can produce medicines for treating human disease.
- Transgenic Animals: can produce medicines in milk (grazing animals); can be used to study the function of a gene of interest.
Gene Therapy: the incorporation of DNA (genes) into human cells for the treatment of a disorder
- potentially replace mutated/nonfunctional genes to treat a disorder.
Chapter 20: Origin
& History of Life
Theories concerning the
evolution of life on earth propose a chemical evolution followed by a
biological evolution
Chemical Evolution: Formation of macromolecules:
-
gases (CH4,
NH3, H2, H2O
(water vapor)) in the primitive interact with energy from volcanoes and
lightning to form small organic molecules (contain carbon and hydrogen (and
oxygen, sulfur, and phosphorus))
- macromolecules form through polymerization of small organic molecules
- macromolecules combine to form organelles
Which
macromolecule was needed first?
3
hypotheses:
1. RNA first
RNA specifies proteins, & can have enzymatic functions
2. Protein first proteins perform most functions inside cell, and can form microspheres that have many properties of a cell
3. Proteins & Nucleic acids formed at roughly the
same time clay served as a substrate
for the polymerization of proteins and RNA (using small organic molecules,
inorganic catalysts (metals), and energy from radioactive decay)
Biological Evolution: The
first cells (protocells) arose from the combination of primitive organelles
(membranes, RNA/protein hybrids (ribosomes)) and existing macromolecules
-
Heterotrophic protocells could have used organic nutrients and
energy sources (ATP?) from the oceans
-
Selection would have
favored those protocells which became capable of producing their own energy
sources from the breakdown of carbohydrates
-
Autotrophic protocells could then have evolved from these more
independent protocells, forming metabolic pathways, and using carbon dioxide
released to form their own carbohydrate molecules
The
first cells then could have arisen
from those protocells, which acquired the ability to self-replicate
History of Life:
The formation of the earth is
dated back to about 4.6 billion years ago
The first prokaryotic cells appeared about 3 billion years ago
Eukaryotic cells evolved about 2.1 billion years ago
Since most eukaryotic cells
carry out aerobic cellular respiration for energy, oxygen in the atmosphere was necessary; hence,
photosynthetic prokaryotes probably preceded the evolution of the first
eukaryotes
Multicellular life forms originated around 700 million years ago
During most of the earthıs
history, only unicellular
organisms were present
Complex organisms arose about 600 million years ago, perhaps the result of the evolution of sexual reproduction in multicellular organisms
Fossils:
Fossils can be dated in
relative terms by the layer of the earth (stratum) in which they consistently appear
-
sedimentation
(weathering and erosion) of rock causes layers to form in the earth
-
the depth of the layers
roughly corresponds to the time elapsed since it was formed
Fossils can be more
absolutely dated by carbon-14 dating,
which measures the amount of the radioisotope carbon-14 remaining in the fossil
in comparison to the amount of its decay product, nitrogen
Paleontology is the science of discovering and studying the fossil
record, and using the results to answer questions about the history of life
Multicellular organisms:
The evolution of an exoskeleton in animals led to diversification of marine invertebrate animals during the Cambrian period (`500 million years ago)
The remainder of the Paleozoic
Era saw the evolution of the first vertebrates, primitive vascular plants and amphibians, as well as
insects, which diversified and flourished
The first mammals appear and
diversify during the Mesozoic era
(50-250 million years ago), during which time the dinosaurs flourished, and
eventually disappeared following a mass extinction
During the Cenozoic era, mammals diversify and flourish; primates, and eventually the first humans evolve during the Neogene period (primates ~ 50 million years ago, and humans ~ 1-2
million years ago)
Presently, we are living in
the Cenozoic Era, Neogene period, Holocene epoch
Factors influencing
evolution:
Continental drift: movement of continents (continual) due to plate
tectonics (movements of plates in the
earthıs crust)
Microevolution vs.
Macroevolution: evolution occurring in more or less
closely related organisms
Environmental Factors: changes in climate affect evolution, giving a
selective advantage to those organisms that can adapt to the changing & new
environment/climate
Mass extinctions:
Causes? Possibilities
are the same factors influencing evolution (above), and other rare and isolated events (meterorite collisions with earth, etc.)
3 in the Paleozoic era, 2 in
the Mesozoic era, as well as a significant mammalian extinction in the Cenozoic era
Geological Time Scale: be familiar with the major divisions (eras and
periods)
Chapter 18: Darwin
and Evolution
1. Age of earth measured in thousands of years vs. millions of
years
2. Each species created individually (appearance and # of species
doesnıt change) vs. species related by descent from common ancestor
(evolutionary history of earth)
3. Adaptations to the environment are the work of the creator
vs. environmental adaptation due to random variations and environmental
conditions
4. Observations must prove the prevailing world view vs.
observations used to test current as well as new hypotheses
Theories of Evolution:
Cuvier: Founder of Paleontology and studies using comparative anatomy
- a series of local catastrophes or mass extinctions led to repopulation by species of surrounding areas, leading to new fossils in a given location over time
Lamarck: adaptation to the environment due to inheritance of acquired characteristics (e.g. the long neck of the giraffe evolved from animals needing to reach food in growing trees, and this trait was inherited to provide an advantage to the offspring in this environment)
Darwin:Descent with modification
Darwin traveled to remote locations and studied similarities and differences in local populations of organisms
Biogeography: the study of the geographic distribution of life
forms on earth
Theory of Natural
Selection: some individuals in a
population gain adaptive characteristics that enable them to survive and
reproduce better than other individuals (concept of fitness ability of an organism to survive and reproduce in
its environment)
-
the adaptive
characteristics are inherited, and enhance survival of those organisms with
this new characteristic, leading to a population of organisms with the adaptive
characteristic
Evidences of Evolution:
-
Fossil Record: fossils can be linked over time since they show a
similarity of form, despite observed changes
-
forms the basis for the Geological
Time Scale
-
Comparative Anatomy: closely related organisms evolved from a common
ancestor (common descent)
-
the study of
similarities and differences in related anatomical features provides a basis
for grouping similar organisms with respect to a common ancestor
-
analogous
structures vs. homologous
structures
- Biochemical Evidence: organisms with more closely related amino acid sequences for the same protein are more closely related evolutionarily
-
studies can include
protein similarities and protein differences
Genetics & Evolution:
-
Variation within a population arises through gene mutations, chromosomal mutations, and recombination
- a population is all the members of one species living in a particular geographical area at the same time
- Only gene mutations result in new alleles, which bring new traits to a population
- Chromosomal mutations and recombination alter the arrangement of genetic information in a cell, and can result in gene mutations
-
Recombination is a rearrangement of genetic information brought
about by sexual reproduction (the result of crossing over between nonsister
chromatids of homologous chromosomes, and independent assortment of maternal
and paternal chromosomes during meiosis, and random union of male and female
gametes during fertilization)
-
Chromosomal mutations include inversions, translocations, and deletions, as well as
chromosome duplications that result in cells with abnormal chromosome numbers
- Hardy-Weinberg
Equilibrium: allele frequencies in a population tend
to remain in equilibrium
- Formula: p2
+ 2pq + q2 =1 (p= frequency of
dominant allele,
q = frequency of recessive allele;
p2=% homozygous dominant individuals, q2=%
homozygous recessive individuals, 2pq=% heterozygous individuals)
- Also,
p + q = 1 if there are only 2
alleles (usually the case)
- Any change in allele frequencies (p and q) in the gene pool of a
population signifies that evolution has occurred
- Gene Pool = every allele of every gene in a population
* see problems - page 305 in text
- Hardy-Weinberg Law: allele frequencies in a gene pool will remain in equilibrium in successive generations of a sexually reproducing population if 5 conditions are met:
- 5
conditions for Hardy-Weinberg equilibrium
1. No mutations
2. No gene flow
3. Random mating
4. No genetic drift
5. No selection
-
All 5 conditions
are rarely met in a given
population resulting in changes in
allele frequencies, and ultimately, microevolution events
1. Mutations:
- Current rates: 2
gene mutations per human gamete
5
x 108 new gene mutations in each human generation
-
some of these mutations may lead to new alleles
2. Gene Flow:
-
the movement of alleles
among populations by the migration of breeding individuals
-
may introduce new
alleles into a population that were produced by mutation in another population
3. Random Mating:
-
individuals pair by
chance and not according to similarity in genotype or phenotype
-
examples of
nonrandom mating:
- inbreeding: mating between relatives to a greater extent than by chance
- assortive
mating: individuals in a population tend to mate with those that
have the same phenotype for a given characteristic (e.g.: mating between
individuals of similar height)
4. Genetic Drift:
-
changes in the allele
frequencies of a gene pool due to chance
-
generally, genetic drift
decreases as population size increases
-
Founder effect: high
frequencies of rare alleles in isolated populations (e.g.: dwarfism
and polydactylism (extra fingers) in Amish populations)
-
Bottleneck effect:
frequencies of certain alleles are increased in a given population due
to major losses of individuals (and alleles) within that population (e.g.:
resulting from natural disaster)
5.
Selection:
-
3 types of natural
selection:
- Directional
selection: extreme phenotypes
favored, due to environmental conditions (e.g.: animal camouflage, bacterial
resistance to antibiotics)
- Stabilizing
selection: intermediate phenotype favored, due to
lack of fitness of extreme phenotypes (e.g.: intermediate birth weights of
infants favored due to high mortality of high & low birth weights)
- Disruptive
selection: 2 or more extreme phenotypes
favored over any intermediate phenotype (i.e.: same as directional selection,
but more than 1 extreme phenotype (for the same or different traits) favored)
-
Variations are maintained to allow populations to adapt to new and changing
conditions (to avoid extinction)
- Allopatric speciation: geographical barriers prevent populations from mating with each other
-
Sympatric speciation: members
of one population develop a genetic difference that prevents them from
reproducing with the original population
-
Adaptive radiation: the
rapid development of many new species from a single ancestral species
(e.g.: 13 species of finches
(birds) of Galapagos Islands are thought to be descendants of a single species
of mainland finches)