EXAM 3 Flashcards
Learn and remember words, concepts, and build on ideas. (112 cards)
1
Q
What stage is gene expression controlled?
A
Transcription initiation
2
Q
What do regulatory proteins do?
A
Modify transcription through blocking (preventing) or facilitating (stimulating) the binding of RNA polymerase to the promoter
3
Q
Where do regulatory proteins gain access to the bases of DNA?
A
At the major groove
4
Q
Gene expression in prokaryotes is due to what?
A
Environmental adaptations; these changes are fully reversible
5
Q
Gene expression in eukaryotes is due to what?
A
Maintaining homeostasis and self-development (i.e. a growing child)
6
Q
How do proteins interact with base-pairs without unwinding the helix?
A
Utilizing the major and minor groove that the helical structure produces.
7
Q
What is accessible in the reading of the major groove?
A
Nucleotides’ hydrogen bond donors and acceptors
8
Q
What are DNA-binding motifs?
A
Regions of regulatory proteins which bind to DNA, necessary for binding in a sequence-specific manner
9
Q
What is the helix-turn-helix motif?
A
Two α-helical segments are linked by a nonhelical segment (called a “turn”)
10
Q
What is the homeodomain?
A
A class of helix-turn-helix, critical in eukaryotic development; first indication that developmental mechanisms are ancient
11
Q
What is the zinc finger motif?
A
Having several forms and occurring in clusters, it uses zinc atoms to coordinate DNA binding
12
Q
What is the leucine zipper motif?
A
Fitting into the major groove, its a region of a subunit interacts with a similar region of another subunit, forming a zipper-like connection
13
Q
How does positive control affect initiation in prokaryotic regulation?
A
The frequency of initiation is increased by activators that stimulate the binding of RNA polymerase to the promoter
14
Q
How does negative control affect initiation in prokaryotic regulation?
A
The frequency of initiation is decreased by repressors that bind to operators (regulatory sites on DNA), preventing/decreasing initiation frequency
15
Q
What is an operon?
A
Multiple genes that are part of a transcription unit having a single promoter
16
Q
What does the lac operon do?
A
Encodes the proteins for the utilization of lactose
17
Q
What does the trp operon do?
A
Encodes the proteins for the synthesis of tryptophan
18
Q
What is induction?
A
The production of enzymes in response to a substrate (i.e. a bacterium encountering lactose and producing enzymes to utilize that lactose)
19
Q
What is repression?
A
The suppression of enzymes in response to a bacteria’s immediate environment (i.e. a bacterium stops synthesizing the enzymes that make tryptophan because it is available in the environment)
20
Q
What does the lac operon consist of?
A
lacZ (β-galactosidase), lacY (permease), lacA (transacetylase), and the lac repressor, lacl
21
Q
How is the lac operon regulated?
A
Negatively by a repressor protein
22
Q
Fill in the blank: In the presence of lactose, an _ molecule binds to the repressor protein, blocking the repressor from _ to the operator, and transcription can now _.
A
inducer, binding, proceed
23
Q
True or False: Even in the absence of lactose, the lac operon is expressed at a very low level.
A
True
24
Q
What is glucose repression and what does it involve?
A
A mechanism for the preference of using glucose over other sugars first. Involves a Catabolite Activator Protein (CAP)
25
What is inducer exclusion in glucose repression?
Presence of glucose prevents entry of lactose, disallowing the lac operon to be induced.
26
What does the trp operon consist of?
Encodes genes to synthesize tryptophan, with the regulatory region located upstream
27
How is the trp operon regulated?
Negatively by the trp repressor protein, encoded outside of the operon: a helix-turn-helix protein that binds to the operator site adjacent to the trp promoter
28
Fill in the blank: Tryptophan binding increases the _ between the two recognition helices, which then allows the repressor to fit into two adjacent portions of the _ _ in DNA.
distance, major, groove
29
Why is control of transcription more complex in eukaryotes than prokaryotes?
Eukaryotes have DNA organized into chromatin, eukaryotic transcription occurs in the nucleus and translation occurs in the cytoplasm which allows for more regulation, and a large amount of DNA is involved since the genes are much larger.
30
What are general transcription factors?
A group of transcription factors necessary for the assembly of an initiation complex by recruiting a RNA polymerase II to a promoter
31
What are specific transcription factors?
These are called activators. Different genes are expressed in different tissues
32
What is the different between general and specific transcription factors?
General TF initiate synthesis at a basal level while specific TF increase the level of transcription higher than the basal level
33
What is a promoter?
Form the binding sites for the general transcription factors, mediating the binding of RNA pol II to the promoter
34
What is an enhancer?
The binding site of the specific transcription factors that acts over large distances by bending DNA to form a loop to position the enhancer closer to the promoter
35
What are coactivators and mediators?
Required structures that bind to TFs and other parts of the transcription apparatus. Mediators not essential to all TFs. The number of coactivators is much less than the number of TFs
36
What is a transcription complex?
A complex of RNA pol II, activators, coactivators, TFs, and other things that work to actively transcribe DNA
37
What are epigenetic alterations?
Alterations in chromatin structure that can permanently shut a gene off
38
Gene expression can be controlled after transcription with...?
Small RNAs (miRNA & siRNA), alternative splicing, RNA editing, and mRNA degradation
39
What does lin-4 encode and do?
Encodes two small RNA molecules, acts as a repressor
40
What is the path of miRNA?
RNA pol II produces pri-miRNA, which folds on itself and get cleaved by Drosha to form pre-miRNA, which exports from the nucleus to get cleaved by Dicer and produces miRNA
41
What is the RNA Induces Silencing Complex (RISC)?
A protein complex where miRNA is loaded into, which represses the expression of genes complementary to the miRNA
42
What is RNA interference?
Small RNA gene silencing, which involves the production of siRNAs
43
How do the production of siRNAs differ to miRNAs?
siRNAs arise from long double-stranded RNA while miRNAs are produced by short double-stranded RNA
44
What is the assumed reason for the evolutionary origin of small RNAs?
To protect the genome
45
What is a similarity of miRNA and siRNA?
They both involve cleavage by the Dicer enzyme, and they both are incorporated into a RISC complex
46
What is the main difference between miRNA and siRNA?
The target: miRNA repress genes different from their origin while siRNAs tend to repress genes they originated from
47
Josef Kölreuter was the first to cross what strains to produce hybrids?
Tobacco
48
Fill in the blanks: T.A. Knight crossed two _-breeding strains of garden _.
true, peas
49
Why were pea plants optimal for Mendel's experiments?
Research showed that pea hybrids could be produced, many pea varieties were available, peas are small and easy to grow, and peas can self-fertilize or be cross-fertilized easily
50
What were Mendel's experimental method (3 stages)?
1. Produce true-breeding strains for each trait he was studying
2. Cross-fertilize the alternate forms of true-breeding strains and perform reciprocal crosses
3. Allow the hybrid offspring to self-fertilize for several generations and count them
51
What is a monohybrid cross?
A cross that follows a single trait with 2 variations
52
What is the first filial generation?
F1, the first generation of hybrid offspring
53
True or False: The recessive trait in a monohybrid cross disappears in the F1 generation.
True
54
What is the second filial generation?
F2, the second generation of hybrid offspring, and where the recessive trait reappears in monohybrid crosses with a phenotypic ratio of 3 dominant:1 recessive
55
What is the phenotypic and genotypic ratio of F2 monohybrid crosses?
Phenotypic - 3:1
Genotypic - 1:2:1
56
Fill in the Blank: Mendel found that traits are not _, and instead are discrete.
intermediate
57
What is Mendel's 5-Element Model?
1. Parents transmit discrete factors (now known as genes)
2. Each individual receives one copy of a gene from each parent
3. Not all copies of a gene are identical due to alleles (homozygous/heterozygous traits)
4. Alleles remain discrete
5. The presence of an allele does not guarantee expression (dominant/recessive)
58
What is the Principle of Segregation?
Two alleles for a gene segregate during gamete formation (one from each parent) and are rejoined at random during fertilization, occurring during meiosis
59
What is a dihybrid cross?
A way to study two variations of two traits in a single cross
60
What is the phenotypic ]ratio of F2 dihybrid crosses?
9:3:3:1
61
What is the Principle of Independent Assortment?
In a dihybrid cross, the alleles of each gene assort independently, and the segregation of different allele pairs is independent
62
What is a testcross?
Crossing an individual of unknown genotype with a homozygous recessive individual
63
What is the Rule of Addition?
The probability that either of two mutually exclusive events occurring is the sum of their individual probabilities; used to find the probability of getting either one outcome OR another
64
What is the Rule of Multiplication?
The probability of two independent events both occurring is the product of their individual probabilities; used to find the probability of events happening together (at the same time)
65
True or False: Dihybrid probabilities are based on monohybrid probabilities.
True
66
Although most genes do not meet these criteria, Mendel's Model of Inheritance assumes that...
Each trait is controlled by a single gene, each gene only has 2 alleles, there is a dominant/recessive relationship between alleles
67
What is phenotypic plasticity?
The production of different phenotypes for the same genotype due to environmental conditions
68
What is continuous variation?
A range of possible phenotypes across genotypes, called a quantitative trait
69
What is pleiotropy?
An allele that has more than one effect on the phenotype
70
True or False: Genes may have more than two alleles in a population, although individuals can only inherit 2 alleles (one from each parent)
True
71
What is incomplete dominance?
An instance in which the heterozygote is intermediate in phenotype between two homozygotes
i.e. red flowers X white flowers = pink flowers
72
What is codominance?
An instance in which the heterozygote shows phenotypic aspects of both homozygotes
i.e. type AB blood
73
An example of both multiple alleles and codominance is the...
Human ABO blood group
74
True or False: Blood group alleles I^A and I^B are NOT codominant.
False: They ARE codominant, making the AB blood type
75
What is epistasis?
When the expression of one gene obscures the effects of another gene
76
What does recessive epistasis result in a phenotypic ratio of?
9:3:4
77
What does dominant epistasis result in a phenotypic ratio of?
9:7
78
True or False: Mendel worked in controlled environmental conditions and viewed traits not affected by environmental factors.
True
79
What is the chromosomal theory of inheritance? Who first came up with it?
Walter Sutton theorized that hereditary traits are carried on chromosomes
80
Fill in the Blanks: Thomas Hunt Morgan correlated the inheritance of a trait with _ chromosomes, and they are called _-linked traits
sex, sex/X
81
What are the sex chromosomes in Drosophila (same as humans)? How about birds? Grasshoppers?
Drosophila/Humans: XX females, XY males
Birds: ZW females, ZZ males
Grasshoppers: XX females, XO males
82
What is an autosome?
A chromosome that isn't a sex chromosome
83
List two attributes of the Y chromosome:
Highly condensed, results in males being hemizygous genotype, few genes are expressed
84
What is a hemizygous genotype?
Recessive alleles on male X chromosome have no active counterpart on Y chromosome
85
True or False, and explain why: X-linked recessive genetic diseases affect males to a greater degree than females.
True because males only require one recessive allele while females require two
86
What is dosage compensation?
Ensures equal expression of genes from sex chromosomes
87
How is dosage compensation accomplished in females?
One X chromosome is randomly inactivated and highly condensed into a Barr body
88
Why are females genetic mosaics? Give an example.
Different X chromosomes are utilized for different cells.
Ex: Calico cats could be all black (X chromosome) or all orange (the other X chromosome) or a mix (heterozygous)
89
True or False: Mitochondria and chloroplasts do NOT contain genes.
False: They DO contain genes
90
What is maternal inheritance?
When genes are passed to offspring solely by the mother
91
What is genetic mapping?
Mapping of the distance between genes that estimates where crossing over occurred between genes
92
What does crossing over do to genes?
It exchanges alleles and results in recombinant combinations
93
What was the conclusion of the Creighton and McClintock Experiment?
A physical exchange of genetic material is accompanied by genetic recombination
94
What did Alfred Sturtevant, undergraduate in Thomas Hunt Morgan's lab, find?
As the physical distance on a chromosome increases, so does the probability of recombination (crossing over)
95
What is the maximum recombination frequency and why?
50% since crossing unlinked genes results in 1:1:1:1 phenotypic ratio
96
How do you calculate recombination frequency? How do you calculate map units and centimorgans?
RF = 100 * [(Recombinant progeny) / (Total progeny)]
1% recombination = 1 map unit (m.u.)
1 map unit = 1 centimorgan (cM)
97
Fill in the Blank: Linked genes are considered "linked" because they are on the same _.
chromosome
98
What happens if homologues undergo two crossovers?
The parental combination is restored and leads to an underestimate of the true genetic distance
99
Fill in the Blanks: Odd numbers of crossover events produce _ gametes while no/even numbers of crossover events produce _ gametes.
recombinant, parental
100
What are chiasmata?
Sites of crossing over
101
What are the hallmarks of an autosomal dominant trait pedigree?
1. Males and females are equally likely to have the trait
2. Traits generally do not skip generations
3. The trait is present whenever the corresponding gene is present
4. There is male-to-male transmission
102
What are the hallmarks of an autosomal recessive trait pedigree?
1. Males and females are equally likely to have the trait
2. Traits often skip generations
3. Both parents of offspring who have the trait are often heterozygotes (carriers)
4. Traits may appear in siblings without appearing in their parents
5. If a parent has the trait, the offspring that do not have it are heterozygous carriers of the trait
103
What are the hallmarks of a X-linked dominant trait pedigree?
1. There is majority male or female affected
2. All daughters of a male who has the trait will also have the trait
3. No male-to-male transmission
4. A female who has the trait may or may not pass the gene to her son/daughter
104
What are the hallmarks of a X-linked recessive trait pedigree?
1. The trait is far more common in males than in females
2. All daughters of an affected male are heterozygous carriers
3. The son of a female carrier has a 50% chance of having the trait
4. No male-to-male transmission
5. Mothers of affected males are either carriers or affected themselves
6. Daughters of female carriers have a 50% chance of being carriers
105
True or False: Multiple amino acid changes in a protein are required to result in a clinical syndrome.
False: Only ONE amino acid change in a single protein can result in a clinical syndrome
106
What is nondisjunction?
The failure of homologues to separate during meiosis, leading to aneuploidy
107
What is aneuploidy?
The loss or gain of a chromosome
108
What is a monosomy?
Losing one copy of an autosome; generally do not survive embryonic development
109
What is a trisomy?
Gaining one copy of an autosome; generally do not survive embryonic development
110
What are the 5 autosomes that trisomic human embryos can survive birth with?
13, 15, 18 - severe defects, typically die within a few months
21 and 22 - survive to adulthood
111
What causes down syndrome? What can influence this?
Trisomy 21; A full third chromosome, a translocation of a part of chromosome 21, and a mother's older age all influence this
112
List and name the possible sex chromosomes due to nondisjunction.
XXX: triple-X females
XXY: males, Klinefelter syndrome
XO: females, Turner syndrome
OY: nonviable zygotes
XYY: males, Jacob Syndrome
