Exam 1 Flashcards
What are the concerns related to the use of GE?
A) New genes introduced in genetically engineered organism may have unpredictable effects on its physiology and biochemistry
B) Transgenic animals can pass their transgene to the offspring
C) Foreign genes may have unexpected and potentially dangerous effects when placed in a genetic environment that is different from what is natural for them
D) All choices are correct
D) All the above
What is the correct chronological order of events?
i. Watson and Crick elucidate the double helix structure of DNA
ii. Friedrich Miescher isolates DNA
iii. Berg, Boyer and Cohen develop the first recombinant DNA molecule
iv. Arber provides evidence for restriction enzyme
v. Gellert discovers DNA ligase enzyme
ii→i→iv→v→iii
In the following biochemical reaction, what are the correct governing equations?
A)
dx/dt = dy/dt = k+xy - k-z
dz/dt = -k+xy + k-z
B)
dx/dt = dy/dt = k+xy
dz/dt = k-z
C) None of these answers are correct
D)
dx/dt = dy/dt = -k+xy + k-z
dz/dt = k+xy - k-z
D)
dx/dt = dy/dt = -k+xy + k-z
dz/dt = k+xy - k-z
Which of the following statements are correct? In the equation: x(t) = xe^kt
If k>0, then it represents exponential growth
What is/are the correct equation(s) that represent the Conservation Law? Select all correct answers.
d(c+a)/dt = 0
d(b+a)/dt = 0
d(b+c)/dt = 0
d(a-c)/dt = 0
d(c+a)/dt = 0
d(b+a)/dt = 0
When considering Michaelis Menten Kinectics’ quasi steady state approximation, what is/are true about the significance of Ɵ?
A) Ɵ is the substrate concentration at which the reaction rate is at half of the maximum
B) Ɵ is a direct measure of the substrate ability for the enzyme (i.e., a large Ɵ indicates that the reaction rate will arrive maximum more quickly)
C) Ɵ is independent on both enzyme and substrate, as well as conditions such as temperature and pH.
D) A and C
A) Ɵ is the substrate concentration at which the reaction rate is at half of the maximum
What is true about Michaelis Menten Kinetics?
A) It is used with quasi steady state approximation when the complex amount stays constant
B) It improves modeling of reaction that does not actually have infinitively exponential growth in real experiment when reactants are limited
C) Both A and B
D) None of the above
C) Both A and B
Which statement is correct about competitive inhibition?
A) primary substrate can bind to the enzyme thus preventing the inhibitor from doing it. The result is that no product can be created.
B) None of these statements are correct
C) Antihistamines are competitve inhibitors of histamines at the histamine receptor
D) Substrate formation rate can be modeled as:
C) Antihistamines are competitve inhibitors of histamines at the histamine receptor
Positively cooperative binding:
n>1, the catalyst’s affinity for ligands increases with more ligands bound to it
Negatively cooperative binding
n<1, the catalyst’s affinity for ligands decreases with more ligands bound to it
Noncooperative binding
n=1, catalyst affinity for ligands is unaffected by the number of ligands bound to it
In a gene circuit diagram, arrows indicate
promotion of a gene
In a gene circuit diagram, T-shaped ends indicate
inhibition of a gene
Gene
A specific nucleotide sequence that is transcribed for RNA
Structural gene
Coding sequence for mRNA in eukaryotes, coregulated by operon
Lac Operon
Bacteria operon (in Escherichia coli) responsible for metabolism of lactose to glucose and galactose
transcriptional terminator
Signals RNA polymerase to stop transcription, downstream of the coding sequence
Exons
Coding segments of eukaryotic DNA for RNA
Introns
Noncoding segments of nucleic acid between coding sequences, removed from primary transcript after RNA polymerase has bound to the promoter and the entire eukaryotic structural gene is transcribed, which links Exons together, eukaryotes
Eukaryote RNA transcription differs because it
has Intron and Exon sequences, ends modified and removed by RNA splicing
Synthetic biology and genetic circuit uses
logic gates
Logic gates are built in gene circuits by
altering or introducing connections between genetic components to make novel regulatory networks
Gene logic gates interpret logical values from
molecular concentrations
NOT gate
changes its output to the opposite state of its input (1 to 0, 0 to 1)
AND gate
takes in 2 inputs and only outputs True if both inputs are True (outputs 1 only if both signals are 1)
OR gate
gives a true signal if one or both of its inputs are true
NAND gate
output is 0 when all inputs are 1 and 1 for all other inputs, inverted AND gate
NOR gate
output is 0 when any input is 0, inverted OR gate
X in logic gates means
exclusive
XOR gate
If a single input is true, the output is true, if both or none are true, the output is false
XNOR gate
If both or neither input is true, the output is true, inverted XOR
Exclusive gates are indicated by
an extra line
Inverted gates are indicated by
a little circle
Logic gates can be used to control genetic circuits with
external inputs (ligands, etc)
Tet-off system
In the presence of doxycycline, tet transactivators (tTAs) cannot bind to the tet-operator (tetO) sequence to induce target gene (transgene) expression. Without Dox, tTAs bind to the tetO sequence to drive target gene expression
Tet-on system
reverse tet transactivators (rtTAs) bind to the tet-operator (tetO) in the presence of Doxycycline to induce transgene expression. Incontrast, in the absence of Dox, rtTAs cannot bind to the tetO and expression does not occur
Operon
a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter, where all genes are transcribed on the same mRNA (must be co-transcribed!)
Promoter
specific region of a gene where RNA polymerase can bind and begin transcription, indicates what mRNA should be transcribed, upstream of the coding sequence
Regulator
control the operator gene in conjunction with inducers and corepressors, not necessarily adjacent to the gene it controls, but produces proteins called repressors that bind to the operator gene and prevent transcription
operator
repressors bind to it, placed between promoter and operon so that repressors physically block transcription
Lac Operon’s two regulatory proteins
Catabolic Activator Protein (CAP) and Lac Repressor Protein
Negative regulation
a repressor protein binds to an operator to prevent a gene from being expressed
positive regulation
the regulation of gene expression by the binding of an activator protein to DNA
Catabolic Activator Protein (CAP)
forms a complex with cAMP to bind to operator site, encourages transcription when glucose is not present (and cAMP is subsequently high)
Lac Repressor Protein
binds to operator to prevent transcription when lactose is not present, binds to allolactose which prevents repression
cAMP is only present when
glucose in the cell is low
Lac operon natural behavior
transcription of lactase when glucose is low and lactose is present but not when glucose is high and/or lactose is low
lac operon is induced
in presence of lactose and absence of glucose, otherwise inert
The lac operon is an example of
negative regulation because it is repressed in the absence of lactose
lacO
operator for lac operon, double regulated by CAP and Lac repressor protein
allosteric regulation
When a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site (ex. Lac repressor protein and allolactose)
Allolactose
Inducer of the lac operon; metabolite of lactose
How to solve first order differential equations
separate variables, integrate both sides, transform equation
equations for x+y=>z with unidirectional rate constant k
dx/dt=-kxy, dy/dt=-kxy, dz/dt=kxy
equations for x+y=>z with bidirectional rate constants k+ and k-
dx/dt= -(k+)xy + (k-)z
dy/dt= -(k+)xy + (k-)z
dz/dt= -(k-)z + (k+)xy
Michaelis-Menten equation
v = (vmax [S])/(Km + [S])
rate equation for a one-substrate enzyme-catalyzed reaction, assumes steady state for enzyme-substrate complex, describes rate of reaction
Conservation laws for x+y=>z
d(x+z)/dt = d(y+z)/dt = 0
steady state approximation
assumes steady concentration of intermediate or enzyme-substrate complex, allows reduction to a scalar ODE, used by michaelis menten
In michaelis menten kinetics, theta is
the amount of substrate when the rate of reaction is half of the maximum, dependent on enzyme, substrate and external conditions, inversely proportional to substrate affinity
How does theta relate to substrate affinity?
inversely, small theta means a strong affinity as it means the reaction proceeds faster (reaches half-maximum rate quicker)
True or false signals are determined by
concentration and threshold
Inducers
external chemicals that interact with gene products, must be present above a concentration threshold to have an effect
During DNA replication, if the base sequence in the template strand is 5’-AGGCTA-3’, which is the correct base sequence in the growing strand?
3’-TAGCCT-5’
What is/are true about Tet system? Select all correct answers
A. Only Tet Off system exist
B. Tet system is typically induced by tetracyclin
C. Both Tet ON and Tet OFF systems exist
D. Doxycycline can be used in place of tetracyclin to induce the Tet system
Tet system is typically induced by tetracyclin, Both Tet ON and Tet OFF systems exist, Doxycycline can be used in place of tetracyclin to induce the Tet system
The phosphate is the ___ end
5’ (Ph sound is the same as five)
The hydroxyl is the ___ end
3’
Which of the following is/are true about an operon?
A. Regulator of an operon are genes that regulate the operator genes
B. Regulator gene controls an operon, but it is not part of an operon
C. Regulator of an operon is where repressor binds to interrupt RNA polymerase from transcribing genes
D. Promoter is the nucleotide sequence in an operon that is recognized by RNA polymerase to initiate transcription for mRNA production
A. Regulator of an operon are genes that regulate the operator genes
B. Regulator gene controls an operon, but it is not part of an operon
D. Promoter is the nucleotide sequence in an operon that is recognized by RNA polymerase to initiate transcription for mRNA production
Which of the following should be considered when one mathematically model a gene regulatory network with ordinary differential equation?
A. Production and degradation rate of mRNA
B. Production and degradation rate of protein
C. Any positive feedback control that could increase the production rate of mRNA
D. Any negative feedback control that could reduce the production rate of mRN
All are correct
What is genetic engineering?
A. All choices are correct
B. It introduces genes that are foreign to the species
C. It is the direct manipulation of an organism’s genes by technological intervention/manipulation
D. It is a term used to describe some modern techniques in molecular biology (recombinant DNA technology)
A. All choices are correct
Genetic engineering is
Direct manipulation of genes through technology
Describes some new techniques in modern biology like recombinant DNA technology
techniques/technology used to modify organisms in order to get them to produce new substances or do new function
Permanently changes genetic makeup of an organism
Difference between genetic engineering and selective breeding
Selective breeding cannot introduce new genes to a species, while genetic engineering can. Breeding uses natural gene changes, while genetic engineering is artificial.
Concerns with genetic engineering vs. selective breeding
Foreign genes can have unexpected and/or dangerous effects in new genetic environments, new genes can have unpredictable effects on physiology and biochemistry of genetically engineered organisms, which could be passed on to offspring
Gregor Mendel (1822-1884)
investigated inheritance in pea plants by observing differences in various traits of the plants from generation to generation, leading to the idea that information needed to build an organism is packaged into units associated with specific dominant and recessive traits
Gregor Mendel found two laws
Law of independent assortment and law of segregation
law of independent assortment
the alleles of two (or more) different genes get sorted into gametes independently of one another
law of segregation
a diploid organism passes a randomly selected allele for a trait to its offspring, such that the offspring receives one allele from each parent.
During DNA replication, if the base sequence in the template strand is 5’-AGGCTA-3’, which is the correct base sequence in the growing strand?
A) 5’-UAGCCU-3’
B) 5’-ATCGGA-3’
C) 5’-AGGCTA-3’
D) 5’-TAGCCT-3’
D) 5’-TAGCCT-3’
What is/are false about Lac Operon? Select all correct answers.
A) IPTG can be used in place of lactose to induce Lac operon
B) Lac operon is ON when lactose is present while glucose is absent
C) Lac operon is OFF when lac repressor is bound
D) Lac operon is ON when glucose is present while lactose is absent
D) Lac operon is ON when glucose is present while lactose is absent
What is the 5’ end?
Phosphate
What is true about Polymerase Chain Reaction (PCR)? Select the best answer.
A) The starting material is DNA
B) The starting material is RNA
C) Each cycle of PCR doubles the amount of nucleic acid in the previous step
D) Both A and C
D) Both A and C
