Study Guide Flashcards
Define Natural Selection
The differential survival and reproduction of individuals
In which of the following processes is apoptosis usually most important?
Morphogenesis
The difference between the top and the bottom in a developing organism is called its
Polarity
The trp operon
Codes for proteins needed for tryptophan synthesis
The earlier the cell intervenes in the process of protein synthesis, the BLANK energy it wastes. Thus, cells will tend to regulate protein synthesis BLANK.
Less; at the earliest stage possible
Sigma factors bind to
RNA polymerases
Actin, which is part of many cellular structures and has several functions, is produced at constant levels in nearly all cells. It is best described as a BLANK protein.
Constitutive
Differentiation consists of
actual biochemical, structural, and functional changes of a cell.
Decent with modification
organisms are produced by their parents but are not identical to them
Common descent
means all living things on Earth are related and come from one common, single ancestor
why did scientists and philosophers have a hard time accepting the notion of common descent?
you cannot get order and complexity from random chaos alone
Regulation of gene expression
Cells only make certain proteins when they are needed
Five ways to silence protein expression
o Downregulate mRNA transcription o Hydrolyze mRNA, preventing translation o Prevent mRNA translation at ribosome o Hydrolyze the protein after it is made o Inhibit the proteins function
Explain beginning of gene expression in Prokaryotes
o Begins at Promoter
o RNA polymerase binds to initiate transcription
o Selective gene transcription
2 regulatory proteins that bind to DNA: repressor and activator
Negative regulation
Repressor protein prevents transcription
Positive regulation
Activator protein stimulates transcription
E coli
o Must adjust to sudden environmental changes
o Changes in nutrients (glucose vs lactose) = metabolic challenge
What is the preferred energy source by E coli? Why?
Glucose- easiest sugar to metabolize
What happens if Glucose is present?
Lactose will not be broken down
Lactose is what?
B-galactoside
What is a B-galactoside?
Disaccharide containing galactose B-linked to glucose
Inducible proteins
Proteins made in response to environment
Constitutive proteins
Proteins made at a constant rate in cell, regardless of environment
Operon
Gene cluster with single promoter that is transcribed as one mRNA
Lac operon
Metabolizes or breaks down lactose
If glucose is present, the lac operon is induced by what?
Lactose
The lac operon is what kind of system?
Inducible
Components of the lac operon
LacO, LacZ, LacY, LacA, LacI
LacO
Operator
Under no lactose conditions, the operator is (blank)
Bound by repressor
When repressor is bound by its inducer, the operator is
empty
LacZ
Gene for B-galactosidease
codes protein that breaks down lactose into galactose and glucose
LacY
Gene for permease
allows lactose to enter
LacA
Gene for trasacetylase
clears toxic material that results from lactose breakdown
LacI
Gene for repressor protein that binds operator
The lac operon is positively regulated by (blank)
CRP
CRP
cAMP receptor protein
when bound to cAMP, CRP (blank)
binds the lac operon promoter and forces RNA polymerase to transcribe the genes of the lac operon
why is the control of RNA polymerase by CRP necessary?
Ensures cell doesn’t transcribe genes to breakdown lactose when it can use glucose instead
cAMP levels are controlled by (blank)
glucose levels
If glucose is high, cAMP is (blank)
low
Low cAMP levels mean that
CRP cannot bind promoter and lac operon is not activated even if lactose present
If glucose is low, cAMP is (blank)
high
High cAMP levels mean that
It binds CRP and CRP binds promoter, promoting transcription of lac operon
Other systems of E coli besides the inducible lac operon system are
repressible systems
Repressible systems
o Repressed only under specific conditions
o Repressor normally not bound to operator
Co-repressor binds to repressor it causes
Repressor to change shape and bind to the operator which inhibits transcription
What is an example of a co-repressor working in a repressible system?
trp operon
Trp operon
Structural genes catalyze the synthesis of the amino acid typtophan
Repressible systems are common in (blank)
anabolic or building pathways
When tryptophan is present in the cell in adequate concentrations, it is (blank)
Advantageous to stop making the enzymes for tryptophan synthesis
How does the cell stop making enzymes for tryptophan synthesis?
Cell uses repressor that binds to operator in trp operon only when its shape is changed by binding to tryptophan (co-repressor)
Consensus sequence
Common sequences within promoters that allow RNA polymerases to bind
What is a very common consensus sequence?
TATA box
Sigma factors
Proteins in prokaryotic cells that bind to RNA polymerase and direct it to specific classes of promoters
RNA polymerase must be bound to a sigma factor before it can
Recognize a promoter and begin transcription
Seven ways to regulate protein expression in Eukaryotes
o Remodel chromatin o Transcriptional control o Processing control o Transport control o mRNA stability control o translational control o protein degradation
initiation of eukaryotic transcription with general transcription factor complex
o TFIID binds to TATA box
o TFIIB binds both RNA polymerase and TFIID and helps identify the transcription initiation site
o TFIIF prevents nonspecific binding of the complex to DNA and helps recruit RNA polymerase to the complex- similar in function to a bacterial sigma factor
o TFIIE binds to the promoter and stabilizes denaturation of DNA
o TFIIH opens the DNA for transcription
What happens in addition to general transcription factor complex?
enhancers and silencers
Enhancers
Regulatory sequences that bind transcription factors that activate transcription or increase rate of transcription
Silencers
Bind transcription factors that repress transcription
Transcription factors have common (blank) in the domains that bind to DNA
structural motifs
What is a common structural motif?
helix turn helix
For DNA recognition, the structural motif must
o Fit into a major or minor groove
o Have amino acids that can project into interior of double helix
o Have amino acids that can bond with interior bases
Development involves (blank)
Distinct but overlapping processes
Four processes of development
Determination
Differentiation
Morphogenesis
Growth
Determination
o Sets fate of cell
o Before any characteristics observable
Example of determination
mesenchymal stem cells fate to become connective tissue determined
differentiation
different types of cells arise, leading to cells with specific structures and functions
example of differentiation
mesenchymal stem cells differentiate to become muscle, fat, tendon, or other connective tissue cells
morphogenesis
organization and spatial distribution of differentiated cells into multicellular body and organs
growth
increase in size of body and its organs by cell division and enlargement
transplantation experiments using amphibian embryos show that (blank)
the fate of cells is determined as the early embryo develops
donor tissue from early-stage embryo
o adopts fate of the new surroundings
o cell fate not determined and is influenced by extracellular environment
donor tissue from older embryo
o continues original path
o cell fate already determined and not influenced by extracellular environment
cell fate
internal decision each undifferentiated cell makes to become part of a particular type of tissue
cell fate determination is influenced by (blank)
gene expression and the extracellular environment
determination is a (blank)
commitment
determination is followed by (blank)
differentiation
differentiation, the changes in (blank)
biochemistry, structure, and function that result in different cell types
cell potency
potential to differentiate into other cell types
totipotent
any cell type (early embryo)
pluripotent
most cell types but not new embryos
multipotent
several related cell types
unipotent
only one cell type (own)- mature
2 processes that drive determination
o Cytoplasmic segregation (unequal cytokinesis) o Induction (cell to cell communication)
Cytoplasmic segregation
Factor may be unequally distributed within cytoplasm and after division it ends up in some cells but not others
Cytoplasmic segregation sets up
polarity
polarity
Developing a “top” and a “bottom”
induction
Factor actively produced and secreted by certain cells to induce other cells to become determined
Cells in a developing embryo influence one another’s developmental fate via (blank)
chemical signals and signal transduction mechanisms
The vertebrate eye development example is an example of (blank)
induction
Concentration gradient of inducer matters as part of induction- example
Highest LIN-3 released by anchor cells in developing C elegans drives primary vulval development
How do signals impact gene expression?
o Concentration of inducer affects degree to which transcription factor is activated
o Inducer acts by binding to receptor on target cell which is followed by signal transduction involving transcription factor activation or translocation of transcription factor from cytoplasm to nucleus
o Signal transduction acts to stimulate expression of genes involved in cell differentiation
pattern formation
Process that results in the spatial organization of tissues and organisms
Pattern formation is linked to
morphogenesis
Morphogenesis involves cell division and differentiation as well as (blank)
apoptosis
Pathways in apoptosis used in morphogenesis
o CED-9 and Bcl-2 = pro survival factors that bind and sequester pro-death factors CED-4 and Apaf1
o If conditions warrant apoptosis, CED-9 and Bcl-2 release CED-4 and Apaf1 which activate apoptosis pathway
What are the four organs of a flower?
Carpels, stamens, petals, and sepals
Organs of a flower grow in (blank) that develop from the floral meristem
whorls
Floral organs are determined by 3 classes of (blank)
organ identity genes
Organ identity gene polypeptide products combine in pairs to form (blank)
transcription factors
A protein called (blank) controls transcription of organ identity genes
LEAFY
The concentration gradient of a diffusible morphogen signals each cell to (blank)
specify its position
Fate of a cell is often determined by (blank)
where the cell is
Positional information often comes in the form of an inducer called a (blank) which (blank)
Morphogen- diffuse from one group of cells to another, setting up concentration gradient
A morphogen directly affects (blank)
target cells
Different concentrations of morphogen cause (blank)
different effects
example of morphogen
o Shh in limb development
o Zone of polarizing activity (ZPA) in limb bud of embryo secretes morphogen Shh and cells in the bud form different limbs (thumb, fingers) depending on concentration of Shh
Higher dose of shh means
little finger
lower dose of shh means
thumb
3 classes of genes involved in determination
maternal effect
segmentation
hox
maternal effect genes
Set up the major axes (anterior/posterior and dorsal/ventral) of egg
Where are maternal effect genes transcribed?
Mothers ovary- mRNA passed to egg
What are genes that help determine the anterior-posterior axis of embryo?
bicoid and nanos
Maternal effect genes are subject to (blank)
unequal distribution
Bicoid mRNA is translated into (blank)
bicoid protein
bicoid protein
Transcription factor that diffuses away from the anterior end, establishing a gradient in the egg cytoplasm
(blank) transports the nanos mRNA from anterior end of egg to the (blank)
Egg’s cytoskeleton; Posterior end
The mRNAs for bicoid and nanos diffuse from where into where?
mother’s cells into anterior end
hunchback
mRNA distributed evenly first, then nanos inhibits translation and bicoid stimulates it which establishes a gradient
after the anterior and posterior ends have been established, the next step in pattern formation is
determination of segment number and locations
segmentation genes
determine the boundaries and polarity of each segment
3 classes of segmentation genes
o Gap genes
o Pair rule
o Segment polarity
gap genes
Organize broad areas; mutations result in omission of body segments
pair rule genes
Divide embryo into units of 2 segments each; mutations result in every other segment missing
segment polarity
Determine boundaries and anterior/posterior organization in individual segments
hox
Determine which organ will be made a given location
Hox genes encode (blank)
Transcription factors that are expressed into different combinations that determine fate of each segment
stem cells
Rapidly dividing, undifferentiated cells that differentiate into several cell types
In plants, stem cells are in the
meristem
In mammals, stem cells occur in
Tissues that need frequent replacement (skin, blood, intestinal lining)
evolution
Change in genetic composition of populations over time
Evolutionary change is observed in
Lab experiments, natural populations, and the fossil record
Genetic changes drive
The origin and extinction of species and the diversification of life
Evolutionary theory
Understanding of the mechanisms of evolutionary change
Darwin 5 year voyage on HMS Beagle
Studied rocks and observed/collected plants and animals
What did Darwin observe in the Galapagos islands
Species similar to mainland of South America but varied island to island
Darwin 3 propositions
o Species change over time
o Descent with modification (common ancestor and diverged over time)
o Natural selection
Natural selection
Differentiation survival and reproduction of individuals based on variation in their traits
Alleles
Different forms of a gene
Locus
Where alleles exist- particular site on chromosome
Gene pool
Sum of all copies of all alleles at a loci in a pop
Gene pool contains what
Genetic variation that produces the phonotypic traits on which natural selection acts
Do individuals or populations evolve?
populations
Group of individuals of a single species that live and interbreed in a particular geographic area
population
mechanisms of evolution
o Natural selection o Mutations o Gene flow o Genetic drift o Nonrandom mating
Natural selection acts on
phenotype
Fitness
Reproductive contribution of a phenotype to subsequent generations relative to other phenotypes
Changes in (blank) of different phenotypes lead to change in allele frequencies
relative success
Fitness of a phenotype is determined by
Relative rates of survival and reproduction of individuals with certain phenotype
3 ways natural selection acts on quantitative traits
o Stabilizing selection
o Directional selection
o Disruptive selection
Stabilizing selection
Preserves average phenotype
Example of stabilizing selection
birth weight
Directional selection
Favors individuals that vary in one direction
Example of directional selection
texas longhorn
Disruptive selection
Favors individuals that vary in both directions from mean
example of disruptive selection
Black bellied seed crackers
mutation
Any change in nucleotide sequences of DNA
Selection acting on random variation results in
adaptation
If conditions change, a mutation could become (blank)
advantageous
Mutations can restore
genetic variation
Mutation adds (blank) to the gene pool
new alleles
allele frequency
Proportion of an allele in the gene pool
genotype frequency
Proportion of each genotype in the population
gene flow
Result of the migration of individuals movement of gametes between populations
example of gene flow
Modern humans expand range into range of Neanderthals- interbreeding resulted in gene flow
genetic drift
Results from random changes in allele frequencies
Because of genetic drift, harmful alleles may (blank) and rare advantageous alleles may (blank)
Harmful alleles; lost
Genetic drift is significant in
small populations
population bottleneck
Environmental conditions result in survival of only a few individuals which can reduce genetic variation
founder effect
Colonizing population unlikely to have all alleles present in whole population
Nonrandom mating occurs when
Individuals choose mates with particular phenotypes
Sexual selection
Favors traits that increase the chances of reproduction
What did Darwin propose about sexual selection?
Traits such as bright colors, long tails, and elaborate courtship displays may improve ability to compete for mates or to be more attractive to the opposite sex
Sexual selection may (blank)
Reduce chances of survival
Evolutionary change can be measured by
Allele and genotype frequencies
If a locus has two alleles, A and a, there could be three genotypes: AA, aa, and Aa. The population is (blank) at that locus.
Polymorphic
p +q =
1
If certain conditions are met, the (blank) of a population does not change over time
genetic structure
Hardy-Weinberg equilibrium
Describes a model situation in which allele frequencies do not change
(blank) can be predicted from allele frequencies
genotype frequencies
conditions of HW
o No mutation (alleles present don’t change and no new alleles added)
o No selection among genotypes (individuals with different genotypes have equal survival and reproduction rates)
o No gene flow (no movement of individuals or gametes into or out of population)
o Population size infinite (smaller genetic drift effect)
o Mating is random (individuals don’t preferentially choose mates based on certain genotypes)
Hardy-Weinberg equilibrium equation
P^2+2pq+q^2 = 1
In HW equation p^2 =
Homozygous dominant (AA)
In HW equation 2pq=
Heterozygous (Aa)
In HW equation q^2 =
Homozygous recessive (aa)
Neutral allele
Allele that does not affect fitness
Sexual reproduction through recombination
o Results in new combinations of genes through the combination of gametes, crossing over, and independent assortment
o Produces genetic variety that increases evolutionary potential
Major pitfall of sexual reproduction
Recombination can break up adaptive gene combinations
Major advantage of sexual reproduction
Sexual recombination generates new combinations of alleles on which natural selection can act
Frequency dependent selection
Polymorphism can be maintained when fitness depends on its frequency in population
Example of frequency dependent selection
Right or left leaning jaw on fish
Four ways to produce and maintain genetic variation
o Neutral mutation
o Sexual reproduction through recombination
o Frequency dependent selection
o Environment and geography
Difficulties of the theory of evolution
o Absence or rarity of translational varieties (should be a record of species that came between ancestor and current species) o Organs of extreme perfection such as eyes o Instinct (thought instants were habits acquired by parents and passed to next gen)
Evidence for common origin
o Morphology
o Embryology
o Rudimentary (vestigial) organs
Morphology
Homology exists across life
Embryology
Similarity between embryos early in development
Rudimentary (vestigial) organs
Organs that lost original function (evolutionary baggage)
Binding of operator prevents (blank) under no lactose conditions
Lac operon from activating
