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What is the purpose of transcription? –
transfer of genetic information from DNA by the synthesis of an RNA molecule copied from the DNA template
What is meant by the template
vs. non-template (or coding) strand? –
The template strand of DNA is the strandcopied to create the RNA strand. Thenon-template/coding strand is the DNA strand that has the same nucleotidesequence as the RNA created (can read the RNA code from the coding strand withT=U)
What is meant by upstream vs. downstream elements?
In general, where is it (promoter) located?
upstream of coding region
What is meant by a consensus sequence?
- a set of proteins, or nucleotides in deoxyribonucleic acid (DNA), that
- appears regularly
What are the functions of a promoter?
to signal the RNa polymerase where to start transcribing the DNA.
In bacteria, what is a sigma factor?
What is its function?
A protein, a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Varies based on target gene.
What molecule carries out the polymerization reaction in transcription?
The core enzyme (does she want something more specific?)
In what direction does polymerization of RNA occur? In what direction does
the transcription bubble move?RNA
elongation proceeds in the 5'—>3' direction
(i.e. the polymerase moves along the template strand of DNA in the 3'—>5' direction) (does this answer both?)
Describe the process of rho-dependent termination in bacteria. What is the rho
factor and what is its function?
rho factor is a protein that acts as a helicase – unwinds the DNA-RNA hybrid in transcription bubble (maybe add a bit more)
What kind of DNA sequence pattern produces a hairpin loop in the RNA transcript?
Mirror structors ie CCTGCXXXXXXXGCAGG
What is the basic structure of transfer RNA?
Clover leaf structures
Why must gene expression be regulated in all organisms? In multicellular organisms in particular?
- –Gene control occurs on many
- levels (Compact DNA-relaxed DNA-pre mRNA- processed mRNA- inactive
- protein, active modified protein), focuses on activating and processing
- correct proteins from genes
Distinguish between negative vs. positive control in gene regulation. Distinguish between inducible vs. repressible systems.
Negative gene control: Has a repressor bound to DNA that needs to be inactivated by an inducerPositive control: Has an activator that needs to be activated by a molecule to bind to DNA and start transcriptionInducible system/operon: transcription is off by default and is turned on in the presence of an inducer moleculeRepressible system/operon: transcription is on by default and turned off in the presence of a molecule
gene encodes regulatory protein (makes repressors and activators)
gene we are regulating; involved in a process or structure (gene being transcribed on DNA)
either a repressor or activator; involved in activating or repressing transcription in DNA
where a regulator protein binds to; a stretch of DNA upstream from +1 site (near promotor)
Upstream regulatory region:
Where the regulatory gene and element are located
location of the structural genes where transcription occurs
What is an operon?
All the structural and regulatory genes and regulatory elements combined, the entire unit
What is the major function of the lac operon in cell metabolism?
-To metabolize lactose (asugar/disaccharide)
What is the function of the repressor gene in the lac operon?
The repressor gene (lac1) codes for the repressor (active regulator protein) through transcription and translation;
What is the function of the operator sequence?
The operator sequence: the regulatory element where the repressor binds to when inactive
What is the function of the promoter in the lac operon?
- Promoter: Where RNA
- polymerase attaches to DNA to begin transcription
What is the function of the repressor gene, operator sequence, promoter, structural genes in the lac operon?
- Structural genes: Genes that code for enzymes
- (B-Galactosidase, Permease, Transacetylase) that break lactose apart to provide glucose (and galactose)
What do the structural genes of the lac operon code for? -
enzymes(B-Galactosidase, Permease, Transacetylase)
Does the repressor exhibit negative or positive control? -
Negative control (repressor)
Is this form of regulation inducible or repressible?-
Inducible (initially off and turned on)
How does the CAP regulation system affect expression of the lac operon structural genes?
- The CAP activator protein influences/speeds up gene expression by promoting transcription when glucose is needed. Without active CAP,
- transcription will not occur.
What is the role of cyclic AMP in this system, and how does glucose affect levels of cAMP?
- Cyclic AMP is made from Adenylyl cyclase breaking apart ATP and making
- the cyclic AMP; cyclic AMP binds to the CAP activators to make them
- active proteins, allowingthem to bind to the regulatory element. When
- glucose levels are low, more cAMP is produced to influence more
- transcription, and less cAMP is is provided when glucose levels are
What is the regulator protein in this example of gene regulation?
The CAP is an activator.
What is a mutation?
a heritable change in genetic information; a change in nucleotide sequence that can alter genetic expression
Distinguish between a somatic
and a germline mutation.
- What are the potential consequences of each? -A somatic mutation occurs in somatic cellsthat
- pass mutations during mitosis, creating a population of mutated cells.
- A germline mutation occurs when mutations in gamete cells pass
- mutations through sexual reproduction, causing all cells in the
- offspring to have the mutation.
What is a base substitution?
-One nucleotide is replaced/substituted because of error in replication. Can be transition or transversion
What is the difference between
a transition and a transversion?
- -A transition (more common) is the replacement of a purine with another purine (A and G) or a pyrimidine with a pyrimidine (C and T). A transversion is the
- replacement of a purine with a pyrimidine or a pyrimidine with a purine.
What is an insertion or deletion?
An insertion is when a nucleotide is added into the sequence, and a deletion is when a nucleotide is removed.
What kind of insertion or deletion causes a frameshift?
-When 1 to2 nucleotides are added or removed (not a multiple of 3, or codon amounts) the entire nucleotide sequence is shifted. Error occurs for the rest of the coding strand.
Can a base substitution cause a
No, it only effects the onecodon the base substitution is located in
What is an expanding trinucleotide repeat?
By what specific process are these thought to arise? -When the same code (same codon) within a nucleotide sequence repeats over and over, the transcribed mRNA can slip during transcription and attach to itself,forming a loop. Replication continues,so the final mRNA has more of the repeated sequence than the DNA (causes erroror problems when translated) (example: Huntington’s disease)
A base substitution causes one codon to turn into a stop codon, which will end translation early and form incompleteproteins.
A base substitution changes the results in one amino acid (makes a different amino acid) which may or may not change the created protein function
There is no change in the final amino acid or protein when a base substitution occurs
At which codon position is a base
substitution most likely to be a silent mutation? Explain.
–Usually occurs at the 3rd nucleotide of the codon (lastnucleotide), has the least effect on the amino acid matching the codon and mostlikely to code for the same amino acid if the first two nucleotides of thecodon are the same.
results in absence of a functional protein (example: hemophilia)
results in a protein with a different function (example: Huntington’s disease)
usually occurs with recessive genes (2 mutant alleles) since the genes will have so much error that a functional protein is not able to form from the resulting codes
mutations can occur in more dominant genes since they can have less error/mutation to create a functional protein, but the protein can have an altered function.