NCSU GN 311 Exam #4
Binding of the regulator gene product to the DNA is necessary to shut off transcription.
-Negative Inducible -Negative Repressible
Regulator gene product binds DNA in a complex with effector molecules.
-Positive inducible -Negative repressible
Transversion
An alteration in the DNA from an AT base pair to a CG base pair is called a ___.
Transition
An alteration in the DNA from an CG base pair to a TA base pair is called a ___.
Frameshift
An insertion of a single base pair in the DNA strand is called a ___ mutation.
Inducible control works by only turning on transcription when a small molecule binds to the regulatory protein; repressible control works by only turning off transcription when a small molecule binds the regulatory protein
Compare inducible control and repressible control
Positive control works by a regulatory protein (activator) binding to DNA to stimulate transcription; negative control works by a regulatory protein (repressor) binding to DNA to prevent transcription
Compare positive and negative control
Moves original and repairs DNA (which is what we see in Ac-Ds in maize)
Conservative transposition
Results in Uracil; causes GC to AT transition
Deamination of C
Results in an apurinic site; removes bond at either G or A bases
Depurination
A process called catabolite repression occurs because glucose is preferred by the cell; catabolite repression means operons that are not needed will not be transcribed
Describe what happens when glucose is in the cell?
A mutation that repeats a previous codon with a different amino acid sequence Ex: UCC (Ser) ---> UGC (Cys) ---> AGC (Ser)
Equivalent Reversion (Suppressor Mutation)
A mutation that repeats a previous codon exactly Ex: AAA ---> GAA ---> AAA --->
Exact Reversion mutation
Sxl, the master regulator of sex determination od Drosophilia, is produced based off of whether a a certain ratio of X chromosomes to autosomes exists. There needs to be a 1 to 1 ratio for it to be produced, and if it is, the Drosophilia will have it. If this is made, the tra protein will be made and the fly will be female.
Explain alternative splicing in the context of Drosophilia sex determination
Glycosylases recognize and remove defective bases in an AP site. Then AP endonuclease cleaves the phosphodiester base and removes rest of nucleotide; DNA polymerase then fills the gap and ligase seals the nick
Explain base excision repair
Imprinting is considered an epigenetic modification and involves a methylation of cytosine residues. -It causes gene to be inactive
Explain imprinting in the context of epigenetics
-miRNA is transcribed from a specific gene and targets other genes for regulation, -siRNA is transcribed from a variety of sources and can target the genes that it comes from only. -miRNA inhibits translation - siRNA degrades mRNA
Explain miRNA and siRNA in the eukaryotic regulation context
Enzyme complex UVR endonuclease recognizes distrortion. Strands of DNA are then seperated by single strand binding proteins. Enzyme cleaves sugar phosphate bonds and removes several nucleotides including the defective area; DNA polymerase then fills the gap and ligase seals the nick
Explain nucleotide excision repair
Ac (activator) is a transposable element with functional transposase. Ds (dissociation) does not contain a functional transposase gene so it requires the AC to move
Explain the Ac-Ds system in Maize
A syndrome in which someone has extra copies of trinucleotide CGG on X chromosome
Fragile-X syndrome characteristics
Mutation that leads to a shift in the reading frame; deletion; insertion
Frameshift Mutations; includes ____ and ____
Cell produces protein that is not normally present; either new gene product or gene product in new location/at an inappropriate time during development
Gain of function protein mutation
Occur in reproductive cells and are passed down to half of the members of the next generation, who will carry the mutation in all of their cells
Germ-line mutations
Phosphate groups; methyl groups; acetyl groups; amino groups
Histone modifications during chromatin remodeling can include additions of ____, ____, and ____ but not ____
It can result in different proteins in different tissues/different times in development; therefore, regulating splicing is extremely important to control
How can alternative splicing affect mRNA processing?
Enhancers affect transcription of distant genes; can drive expression of genes at specific places and times
How do enhancers affect eukaryotic gene regulation?
Insulators are cis-elements and while they can't act on distant genes, they block the enhancer function so it cannot
How do insulators affect eukaryotic gene regulation?
-such as shorten the Poly A tail -their interaction with mRNA internal structure is important
How do ribonucleases affect regulation?
Silencers inhibit transcription by binding to elements in the regulatory promoter or distant to the promoter
How do silencers affect eukaryotic gene regulation?
- mRNA cleavage, -inhibition of translation, -transcriptional silencing -slicer independent degradation of mRNA
How does RNAi regulate genes?
FLC is the gene that suppresses flowering when turned on; if you acetylate the gene, it turns on and prevents flowring. Deacetylation allows flowering to occur.
How does flowering in Arabidopsis relate to eukaryotic gene regulation?
Mismatch repair proteins recognize an abnormal helical structure and recognize the incorrect base. Exonucleases remove an area of the new strands to the mismatch; DNA polymerase fills in gap and ligase seals the nick.
How does mismatch repair work?
A disease in which someone has extra copies of trinucleotide CAG
Huntington disease characteristics
Occurs in a different gene (mutation in anticodon of tRNA reverses effects of initial mutation)
Intergenic mutation
Within the same gene
Intragenic mutation
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation in this case refers to...
Methylation of cytosine
Restores correct form to incorrectly methylated guanine bases
Methyltransferase
A mutation that changes the amino acid (may alter protein function or protein is nonfunctional). Neutral is a missense mutation that doesn't affect protein function
Missense (nonsynonymous) mutation and subtype neutral
Uses transposase to move original, but doesn't repair DNA
Nonreplicative transposition
A mutation that changes the codon so that it becomes a stop codon
Nonsense mutation
Results in substitution of 1 base for another
Point mutation
A mutation where a stop codon is changed to a codon that codes for amino acid (results in a longer protein)
Readthrough mutation
DNA sequences that are not transcribed, but play a role in regulating other nucleotide sequences
Regulatory elements
Encode products that interact with other sequences and affect with transcription and/or translation of these sequences
Regulatory genes
Uses transposase to move copy
Replicative transposition
Auxotroph
Requires some chemical for growth; won't grow on minimal media because unable to synthesize a lot of necessary nutrients
Uses reverse transcriptase to create DNA from element's RNA
Retrotransposons
Garrod
Scientist who conducted experiments on Alkaptonuria and diet's effect on it
A mutation that still codes for the same amino acid
Silent (synonymous) mutation
Occur in nonreproductive cells and are passed to new cells through mitosis (some of the cells in organism affected)
Somatic mutations
Encode proteins that are used in metabolism or play a structural role in the cell
Structural genes
Positive Inducible; negative inducible
The type(s) of prokaryotic regulation where: transcription occurs with high effector levels.
Purine to purine or pyrimidine to pyrimidine change; A to G, C to T, etc.
Transition point mutation definition; what base change to what?
Genetic elements that move from one site to another; can alter the phenotype when they move; also called "jumping genes"
Transposable genetic elements
Pyrimidine to purine or purine to primidine; A to C, G to T, etc.
Transversion point mutation definition; what bases change to what?
Alkaptonuria was one of the first disease phenotypes correlated with a genotype. It is characterized by absense of homogentisate oxidase activity.
Was the significance of Alkaptonuria?
Small regions where nucleosome is missing; they serve as binding sites for regulatory proteins
What are DNaseI Hypersensitive sites?
These genes give specific identity to each segment. In Drosophilia, they have two major gene clusters: Antennapedia complex (5 genes) and bithorax complex (3 genes); all of them have common DNA sequences called homeboxes
What are homeotic genes? What are two major gene clusters in Drosophilia? What do they all have in common?
RNA sequences in the mRNA that affect its translation
What are riboswitches?
Whorl 1: Sepals Whorl 2: Petals Whorl 3: Stamens Whorl 4: Carpels
What are the results of a wild-type Arabidopsis flower?
1. Gap genes divide the embryo into broad segments, 2. pair-rule genes affect the same pattern in every other segment, 3. segment polarity genes affect anterior/posterior of each segment
What are the three types of segmentation genes? What do they do?
Either by siding the nucleosome along the DNA or changing the conformation of either the nucleosome or DNA
What are the two ways chromatin remodeling happens?
When thymine bases bond together and distort the helix; this leads to an inhibition in replication
What are thymine dimers?
They bind to other DNA, other transcription factors, and polymerase to regulate transcription
What are transcription factors?
Since transcription is stimulated by light, and light induces RBC, there is an increase in RBC transcripts in leaves after exposure to light
What can affect photosynthesis in plants?
Interact with other proteins, be modified, be localized, be degraded
What can transcription factors do?
Maternal genes (egg polarity genes), which establish anterior/posterior polarity and dorsal/ventral polarity; during development
What comes first in embryological Drosphilia development? When are these transcribed?
Translation of maternal genes hunchback and caudal, which are distributed uniformly along the oocyte
What do bicoid and nanos regulate?
It weakens the interaction with DNA and may allow transcription factors to bind
What does acetylation of tails of histones do?
Cis acting means that the action of an element affects only the genes adjacent to it; the operater and promoter elements are cis acting
What does cis acting mean? What elements of the lac operon are cis acting?
It can either decrease or increase transcription depending on the area methylated
What does methylation of tails of histones do?
Trans acting means that the mutant gene does not have to be adjacent to other genes to affect them; the repressor is trans acting
What does trans acting mean? What elements of the lac operon are trans acting?
Transacetylase
What enzyme does A code for?
Permease
What enzyme does Y code for?
Beta-galactosidase
What enzyme does Z code for?
Bicoid RNA; Nanos RNA; Bicoid stimulates hunchback and represses caudal, while nanos just inhibits hunchback
What gene accumulates at the anterior end? What gene accumulates at the posterior end? What are their main functions?
Levels of cAMP are low, and less likely to bind to CAP. RNA polymerase therefore cannot bind to DNA as well and transcription rate is low.
What happens when glucose in the cell is high?
Levels of cAMP are high, cAMP readily binds CAP, and it results in high rates of transcription and translation. A lot of glucose produced from lactose.
What happens when glucose in the cell is low?
When tryptophan level is high, region 3 pairs with region 4, which terminates transcription
What happens when tryptophan levels are high in the trp operon?
When tryptophan level is low, region 2 pairs with region 3 which inhibits termination and keeps transcription going therefore more tryptophan is made
What happens when tryptophan levels are low in the trp operon?
The attenuator is located in the leader sequence and responsible for decreasing transcription when trp is present
What is the attenuator in the trp operon?
Loosely coiled
What is transcriptionally active DNA like?
DNA polymerase stalls replication so that exonuclease can remove the incorrect nucleotide, making way for DNA polymerase to replace it. This happens during replication.
What repair mechanisms are used during proofreading to repair mistakes? Explain each; when does proofreading happen?
Nucleotide excision repair
What repair system has to be faulty for zeroderma pigmentosum to occur
Proofreading repair; base excision repair
Which repair mechanism(s) involve(s) the removal of a single nucleotide?
Nucleotide excision repair; mismatch repair
Which repair mechanism(s) involve(s) the removal of several nucleotides?
Cis-acting, variable position, variable orientation
Which set of terms applies to enhancers as they are associated with eukaryotic gene regulation?
Functional beta-galactosidase is NOT produced. Functional permease is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is ABSENT and the lac operon genotype is: I+P+O+Z-Y+
Functional beta-galactosidase is NOT produced. Functional permease is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is ABSENT and the lac operon genotype is: I+P-O+Z+Y+
Only functional permease is produced. Functional beta-galactosidase is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is ABSENT and the lac operon genotype is: I-P+O+Z-Y+
Functional beta-galactosidase and functional permease are produced
Will functional permease and beta-galactosidase be produced if lactose is ABSENT and the lac operon genotype is: IsP-O+Z-Y-/I-P+OcZ+Y+
Only functional beta-galactosidase is produced. Functional permease is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is PRESENT and the lac operon genotype is: I+P+O+Z+Y-/IsP+OcZ+Y-
Only functional permease is produced. Functional beta-galactosidase is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is PRESENT and the lac operon genotype is: I+P+OcZ-Y+/I-P+O+Z-Y+
Functional beta-galactosidase is NOT produced. Functional permease is NOT produced
Will functional permease and beta-galactosidase be produced if lactose is PRESENT and the lac operon genotype is: IsP+O+Z-Y+
Results in transitions after replication; mispairing due to flexibility in helix
Wobble Base Pairing
The genes that determine the anterior-posterior axis in the embryo of D. melanogaster are ___ genes.
maternal genes