Study Guide Flashcards
1
Q
Define Natural Selection
A
The differential survival and reproduction of individuals
2
Q
In which of the following processes is apoptosis usually most important?
A
Morphogenesis
3
Q
The difference between the top and the bottom in a developing organism is called its
A
Polarity
4
Q
The trp operon
A
Codes for proteins needed for tryptophan synthesis
5
Q
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.
A
Less; at the earliest stage possible
6
Q
Sigma factors bind to
A
RNA polymerases
7
Q
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.
A
Constitutive
8
Q
Differentiation consists of
A
actual biochemical, structural, and functional changes of a cell.
9
Q
Decent with modification
A
organisms are produced by their parents but are not identical to them
10
Q
Common descent
A
means all living things on Earth are related and come from one common, single ancestor
11
Q
why did scientists and philosophers have a hard time accepting the notion of common descent?
A
you cannot get order and complexity from random chaos alone
12
Q
Regulation of gene expression
A
Cells only make certain proteins when they are needed
13
Q
Five ways to silence protein expression
A
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
14
Q
Explain beginning of gene expression in Prokaryotes
A
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
15
Q
Negative regulation
A
Repressor protein prevents transcription
16
Q
Positive regulation
A
Activator protein stimulates transcription
17
Q
E coli
A
o Must adjust to sudden environmental changes
o Changes in nutrients (glucose vs lactose) = metabolic challenge
18
Q
What is the preferred energy source by E coli? Why?
A
Glucose- easiest sugar to metabolize
19
Q
What happens if Glucose is present?
A
Lactose will not be broken down
20
Q
Lactose is what?
A
B-galactoside
21
Q
What is a B-galactoside?
A
Disaccharide containing galactose B-linked to glucose
22
Q
Inducible proteins
A
Proteins made in response to environment
23
Q
Constitutive proteins
A
Proteins made at a constant rate in cell, regardless of environment
24
Q
Operon
A
Gene cluster with single promoter that is transcribed as one mRNA
25
Lac operon
Metabolizes or breaks down lactose
26
If glucose is present, the lac operon is induced by what?
Lactose
27
The lac operon is what kind of system?
Inducible
28
Components of the lac operon
LacO, LacZ, LacY, LacA, LacI
29
LacO
Operator
30
Under no lactose conditions, the operator is (blank)
Bound by repressor
31
When repressor is bound by its inducer, the operator is
empty
32
LacZ
Gene for B-galactosidease
| codes protein that breaks down lactose into galactose and glucose
33
LacY
Gene for permease
| allows lactose to enter
34
LacA
Gene for trasacetylase
| clears toxic material that results from lactose breakdown
35
LacI
Gene for repressor protein that binds operator
36
The lac operon is positively regulated by (blank)
CRP
37
CRP
cAMP receptor protein
38
when bound to cAMP, CRP (blank)
binds the lac operon promoter and forces RNA polymerase to transcribe the genes of the lac operon
39
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
40
cAMP levels are controlled by (blank)
glucose levels
41
If glucose is high, cAMP is (blank)
low
42
Low cAMP levels mean that
CRP cannot bind promoter and lac operon is not activated even if lactose present
43
If glucose is low, cAMP is (blank)
high
44
High cAMP levels mean that
It binds CRP and CRP binds promoter, promoting transcription of lac operon
45
Other systems of E coli besides the inducible lac operon system are
repressible systems
46
Repressible systems
o Repressed only under specific conditions
| o Repressor normally not bound to operator
47
Co-repressor binds to repressor it causes
Repressor to change shape and bind to the operator which inhibits transcription
48
What is an example of a co-repressor working in a repressible system?
trp operon
49
Trp operon
Structural genes catalyze the synthesis of the amino acid typtophan
50
Repressible systems are common in (blank)
anabolic or building pathways
51
When tryptophan is present in the cell in adequate concentrations, it is (blank)
Advantageous to stop making the enzymes for tryptophan synthesis
52
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)
53
Consensus sequence
Common sequences within promoters that allow RNA polymerases to bind
54
What is a very common consensus sequence?
TATA box
55
Sigma factors
Proteins in prokaryotic cells that bind to RNA polymerase and direct it to specific classes of promoters
56
RNA polymerase must be bound to a sigma factor before it can
Recognize a promoter and begin transcription
57
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
```
58
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
59
What happens in addition to general transcription factor complex?
enhancers and silencers
60
Enhancers
Regulatory sequences that bind transcription factors that activate transcription or increase rate of transcription
61
Silencers
Bind transcription factors that repress transcription
62
Transcription factors have common (blank) in the domains that bind to DNA
structural motifs
63
What is a common structural motif?
helix turn helix
64
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
65
Development involves (blank)
Distinct but overlapping processes
66
Four processes of development
Determination
Differentiation
Morphogenesis
Growth
67
Determination
o Sets fate of cell
| o Before any characteristics observable
68
Example of determination
mesenchymal stem cells fate to become connective tissue determined
69
differentiation
different types of cells arise, leading to cells with specific structures and functions
70
example of differentiation
mesenchymal stem cells differentiate to become muscle, fat, tendon, or other connective tissue cells
71
morphogenesis
organization and spatial distribution of differentiated cells into multicellular body and organs
72
growth
increase in size of body and its organs by cell division and enlargement
73
transplantation experiments using amphibian embryos show that (blank)
the fate of cells is determined as the early embryo develops
74
donor tissue from early-stage embryo
o adopts fate of the new surroundings
| o cell fate not determined and is influenced by extracellular environment
75
donor tissue from older embryo
o continues original path
| o cell fate already determined and not influenced by extracellular environment
76
cell fate
internal decision each undifferentiated cell makes to become part of a particular type of tissue
77
cell fate determination is influenced by (blank)
gene expression and the extracellular environment
78
determination is a (blank)
commitment
79
determination is followed by (blank)
differentiation
80
differentiation, the changes in (blank)
biochemistry, structure, and function that result in different cell types
81
cell potency
potential to differentiate into other cell types
82
totipotent
any cell type (early embryo)
83
pluripotent
most cell types but not new embryos
84
multipotent
several related cell types
85
unipotent
only one cell type (own)- mature
86
2 processes that drive determination
```
o Cytoplasmic segregation (unequal cytokinesis)
o Induction (cell to cell communication)
```
87
Cytoplasmic segregation
Factor may be unequally distributed within cytoplasm and after division it ends up in some cells but not others
88
Cytoplasmic segregation sets up
polarity
89
polarity
Developing a “top” and a “bottom”
90
induction
Factor actively produced and secreted by certain cells to induce other cells to become determined
91
Cells in a developing embryo influence one another’s developmental fate via (blank)
chemical signals and signal transduction mechanisms
92
The vertebrate eye development example is an example of (blank)
induction
93
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
94
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
95
pattern formation
Process that results in the spatial organization of tissues and organisms
96
Pattern formation is linked to
morphogenesis
97
Morphogenesis involves cell division and differentiation as well as (blank)
apoptosis
98
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
99
What are the four organs of a flower?
Carpels, stamens, petals, and sepals
100
Organs of a flower grow in (blank) that develop from the floral meristem
whorls
101
Floral organs are determined by 3 classes of (blank)
organ identity genes
102
Organ identity gene polypeptide products combine in pairs to form (blank)
transcription factors
103
A protein called (blank) controls transcription of organ identity genes
LEAFY
104
The concentration gradient of a diffusible morphogen signals each cell to (blank)
specify its position
105
Fate of a cell is often determined by (blank)
where the cell is
106
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
107
A morphogen directly affects (blank)
target cells
108
Different concentrations of morphogen cause (blank)
different effects
109
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
110
Higher dose of shh means
little finger
111
lower dose of shh means
thumb
112
3 classes of genes involved in determination
maternal effect
segmentation
hox
113
maternal effect genes
Set up the major axes (anterior/posterior and dorsal/ventral) of egg
114
Where are maternal effect genes transcribed?
Mothers ovary- mRNA passed to egg
115
What are genes that help determine the anterior-posterior axis of embryo?
bicoid and nanos
116
Maternal effect genes are subject to (blank)
unequal distribution
117
Bicoid mRNA is translated into (blank)
bicoid protein
118
bicoid protein
Transcription factor that diffuses away from the anterior end, establishing a gradient in the egg cytoplasm
119
(blank) transports the nanos mRNA from anterior end of egg to the (blank)
Egg’s cytoskeleton; Posterior end
120
The mRNAs for bicoid and nanos diffuse from where into where?
mother's cells into anterior end
121
hunchback
mRNA distributed evenly first, then nanos inhibits translation and bicoid stimulates it which establishes a gradient
122
after the anterior and posterior ends have been established, the next step in pattern formation is
determination of segment number and locations
123
segmentation genes
determine the boundaries and polarity of each segment
124
3 classes of segmentation genes
o Gap genes
o Pair rule
o Segment polarity
125
gap genes
Organize broad areas; mutations result in omission of body segments
126
pair rule genes
Divide embryo into units of 2 segments each; mutations result in every other segment missing
127
segment polarity
Determine boundaries and anterior/posterior organization in individual segments
128
hox
Determine which organ will be made a given location
129
Hox genes encode (blank)
Transcription factors that are expressed into different combinations that determine fate of each segment
130
stem cells
Rapidly dividing, undifferentiated cells that differentiate into several cell types
131
In plants, stem cells are in the
meristem
132
In mammals, stem cells occur in
Tissues that need frequent replacement (skin, blood, intestinal lining)
133
evolution
Change in genetic composition of populations over time
134
Evolutionary change is observed in
Lab experiments, natural populations, and the fossil record
135
Genetic changes drive
The origin and extinction of species and the diversification of life
136
Evolutionary theory
Understanding of the mechanisms of evolutionary change
137
Darwin 5 year voyage on HMS Beagle
Studied rocks and observed/collected plants and animals
138
What did Darwin observe in the Galapagos islands
Species similar to mainland of South America but varied island to island
139
Darwin 3 propositions
o Species change over time
o Descent with modification (common ancestor and diverged over time)
o Natural selection
140
Natural selection
Differentiation survival and reproduction of individuals based on variation in their traits
141
Alleles
Different forms of a gene
142
Locus
Where alleles exist- particular site on chromosome
143
Gene pool
Sum of all copies of all alleles at a loci in a pop
144
Gene pool contains what
Genetic variation that produces the phonotypic traits on which natural selection acts
145
Do individuals or populations evolve?
populations
146
Group of individuals of a single species that live and interbreed in a particular geographic area
population
147
mechanisms of evolution
```
o Natural selection
o Mutations
o Gene flow
o Genetic drift
o Nonrandom mating
```
148
Natural selection acts on
phenotype
149
Fitness
Reproductive contribution of a phenotype to subsequent generations relative to other phenotypes
150
Changes in (blank) of different phenotypes lead to change in allele frequencies
relative success
151
Fitness of a phenotype is determined by
Relative rates of survival and reproduction of individuals with certain phenotype
152
3 ways natural selection acts on quantitative traits
o Stabilizing selection
o Directional selection
o Disruptive selection
153
Stabilizing selection
Preserves average phenotype
154
Example of stabilizing selection
birth weight
155
Directional selection
Favors individuals that vary in one direction
156
Example of directional selection
texas longhorn
157
Disruptive selection
Favors individuals that vary in both directions from mean
158
example of disruptive selection
Black bellied seed crackers
159
mutation
Any change in nucleotide sequences of DNA
160
Selection acting on random variation results in
adaptation
161
If conditions change, a mutation could become (blank)
advantageous
162
Mutations can restore
genetic variation
163
Mutation adds (blank) to the gene pool
new alleles
164
allele frequency
Proportion of an allele in the gene pool
165
genotype frequency
Proportion of each genotype in the population
166
gene flow
Result of the migration of individuals movement of gametes between populations
167
example of gene flow
Modern humans expand range into range of Neanderthals- interbreeding resulted in gene flow
168
genetic drift
Results from random changes in allele frequencies
169
Because of genetic drift, harmful alleles may (blank) and rare advantageous alleles may (blank)
Harmful alleles; lost
170
Genetic drift is significant in
small populations
171
population bottleneck
Environmental conditions result in survival of only a few individuals which can reduce genetic variation
172
founder effect
Colonizing population unlikely to have all alleles present in whole population
173
Nonrandom mating occurs when
Individuals choose mates with particular phenotypes
174
Sexual selection
Favors traits that increase the chances of reproduction
175
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
176
Sexual selection may (blank)
Reduce chances of survival
177
Evolutionary change can be measured by
Allele and genotype frequencies
178
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
179
p +q =
1
180
If certain conditions are met, the (blank) of a population does not change over time
genetic structure
181
Hardy-Weinberg equilibrium
Describes a model situation in which allele frequencies do not change
182
(blank) can be predicted from allele frequencies
genotype frequencies
183
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)
184
Hardy-Weinberg equilibrium equation
P^2+2pq+q^2 = 1
185
In HW equation p^2 =
Homozygous dominant (AA)
186
In HW equation 2pq=
Heterozygous (Aa)
187
In HW equation q^2 =
Homozygous recessive (aa)
188
Neutral allele
Allele that does not affect fitness
189
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
190
Major pitfall of sexual reproduction
Recombination can break up adaptive gene combinations
191
Major advantage of sexual reproduction
Sexual recombination generates new combinations of alleles on which natural selection can act
192
Frequency dependent selection
Polymorphism can be maintained when fitness depends on its frequency in population
193
Example of frequency dependent selection
Right or left leaning jaw on fish
194
Four ways to produce and maintain genetic variation
o Neutral mutation
o Sexual reproduction through recombination
o Frequency dependent selection
o Environment and geography
195
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)
```
196
Evidence for common origin
o Morphology
o Embryology
o Rudimentary (vestigial) organs
197
Morphology
Homology exists across life
198
Embryology
Similarity between embryos early in development
199
Rudimentary (vestigial) organs
Organs that lost original function (evolutionary baggage)
200
Binding of operator prevents (blank) under no lactose conditions
Lac operon from activating
