Unit 6- Continued Flashcards
Gene Regulation
Gene regulation controls which genes are turned on (expressed) and turned off (silenced).
What regulates gene expression in eukaroytes?
transcription factors and how tightly or loosely DNA is coiled around a histone
What is the structure formed when DNA wraps around proteins?
Chromatin
Chromatin is composed of DNA and histones.
What is the effect of tightly coiled DNA (Heterochromatin) on gene expression?
Genes OFF
Tightly coiled DNA hides the gene, preventing RNA polymerase from accessing it.
What chemical modification makes DNA coil tighter, keeping genes OFF?
Methylation
Methylation involves adding a methyl group (CH3) to DNA.
What happens to gene expression when DNA is loosely coiled (Euchromatin)?
Genes ON
Loosely coiled DNA allows RNA polymerase to access the gene for transcription.
What chemical modification loosens DNA structure, turning genes ON?
Acetylation
Acetylation involves adding an acetyl group (Ac) to histones.
What role do transcription factors play in gene expression?
they help the RNA polymerase bind to the promoter
Transcription factors are proteins that interact with DNA to regulate transcription.
What are activators in the context of gene regulation?
Proteins that turn genes ON
Activators bind to enhancers and facilitate RNA polymerase attachment.
What is the function of repressors in gene regulation?
Proteins that turn genes OFF
Repressors bind to silencers to block transcription by RNA polymerase.
Where is a promoter located in relation to a gene?
Just before the gene or upstream of the gene
Promoters are specific DNA sequences where RNA polymerase binds to initiate transcription.
What happens to the promoter when DNA is tightly wrapped around histones?
The promoter is hidden
This prevents RNA polymerase from binding, resulting in the gene being OFF.
What occurs to the promoter when DNA is loosely wrapped around histones?
The promoter is exposed
This allows RNA polymerase to bind, turning the gene ON.
Fill in the blank: Tightly coiled DNA (Heterochromatin) leads to _______.
Genes OFF
Fill in the blank: Loosely coiled DNA (Euchromatin) leads to _______.
Genes ON
Are Promoters located on histones?
no they are located before a gene and they are like a landing pad for RNA polymerase
Promoters are specific DNA sequences, not proteins.
Euchromatin
expressed genes bc the DNA is loosely coiled and the DNA can be transcribed
Heterochromatin
genes that are hidden and not expressed bc the DNA is tightly coiled and DNA can be transcribed
How can we modfiy the histone proteins and DNA?
we can add acetyl groups to the histones and the acetyl groups loosen the histones and then DNA can be transcribed
Histone Deacetylation
removes acetyl groups and turns off transcription
Histone Acetylation
adds acetyl groups and turns on trancription
DNA Methylation
adds methyl groups (CH3) to DNA and ends up coiling DNA around the histone making it go from euchromatin to heterochromatin
How is DNA methylation different from Histone Acetylation?
methylation turns transcription off and makes it go from euchromatin to heterochromatin but acetylation turns transcription on and makes it go from heterochromatin to euchromatin
Epigenetics
how behavior/nutrition can affect gene expression - so there is no genetic code for this
DID U FINISH
YES
What is the function of the promoter?
The promoter is the starting line for transcription, located right next to the gene.
Where is the promoter located?
Before the actual coding sequence of the gene.
What are proximal control elements?
Proximal control elements are located close to the gene, near the promoter.
Where are proximal control elements found?
Right next to the promoter, but still outside the gene’s actual coding sequence.
What are distal control elements?
Distal control elements are far away from the gene but can still affect gene expression.
Where can distal control elements be located?
They can be farther from the gene, sometimes even in regions on other chromosomes.
How do distal control elements affect gene expression?
DNA can bend to bring them closer to the promoter and gene.
What part of the gene is copied into mRNA?
The gene itself.
What do control elements act like around the gene?
Switches that control whether the gene gets turned on or off.
What is the role of the promoter in gene expression?
It acts as an on/off switch right before the gene.
What is the role of proximal control elements in gene expression?
They are close by and adjust the switch.
What is the role of distal control elements in gene expression?
They can boost or block the switch from a distance.
What are activators in the context of eukaryotic gene regulation?
Special proteins that bind to enhancer regions of the DNA.
What is the role of enhancers in gene regulation?
They play a crucial role in regulating gene expression, even though they are far from the gene itself.
What happens to DNA after activators bind to enhancers?
The DNA bends.
Why does DNA bending occur during gene regulation?
To bring the enhancer region closer to the promoter.
What is the promoter in the context of transcription?
The area of the DNA where transcription starts.
How does the bending of DNA assist in transcription?
It helps the activator-bound enhancer interact with the promoter region.
What does RNA polymerase do during transcription?
It attaches to the promoter and starts transcribing the gene into mRNA.
What is mRNA in relation to gene expression?
A copy of the gene that will later be used to make the protein.
Fill in the blank: Activators bind to _______ regions of the DNA.
[enhancer]
True or False: Enhancers are located close to the gene they regulate.
False
What is the first draft of mRNA called?
pre-mRNA
alternative RNA splicing
key step in processing pre-mRNA that allows a single gene to produce multiple different proteins
What are the non-coding regions that are removed during alternative RNA splicing?
introns
What are the coding regions that are stitched together to form the final mRNA?
exons
What happens to introns during alternative RNA splicing?
They are cut out and discarded
What can the cell do with exons during alternative RNA splicing?
Mix and match exons in different ways
What does the final mRNA sequence determine?
Which protein is made
True or False: Alternative splicing allows one gene to code for multiple proteins.
True
Fill in the blank: After transcription, the pre-mRNA must be processed before it can be used to make a _______.
protein
What are the key levels of gene regulation?
Chromatin Level, Transcription Level, RNA Processing Level, Translation Level, Post-Translation Level
These levels indicate that gene expression can be controlled at multiple stages.
What happens at the Chromatin Level of gene regulation?
Histone modification, DNA methylation
Histone acetylation leads to loose chromatin, while methylation results in tight chromatin.
What is the effect of histone acetylation on gene expression?
Leads to loose chromatin
This allows for easier access for transcription factors.
What is the effect of DNA methylation on gene expression?
Turns genes off
Methylation typically inhibits gene transcription.
What regulates whether RNA polymerase can start transcription?
Transcription factors, activators, enhancers
These elements are crucial for initiating the transcription process.
What is alternative splicing?
Creates different proteins from the same gene
This process occurs during RNA Processing Level.
What role do miRNAs and siRNAs play in gene regulation?
Prevent mRNA from being translated
They are important in the Translation Level of gene regulation.
What occurs at the Post-Translation Level of gene regulation?
Proteins can be activated or degraded
This allows for the regulation of protein function after they are synthesized.
Non Coding RNA’s
microRNA repression/stop translation by binding to mRNA ribosomes cannot translate
What is the structure of Prokaryotic DNA?
DNA is floating in the cytoplasm and consists of one circular chromosome.
What characterizes Prokaryotic DNA in terms of coding regions?
Few non-coding regions; almost all DNA codes for proteins.
How are genes organized in Prokaryotes?
Genes are often grouped together in operons for better control.
What is an operon?
A group of genes controlled together, acting like a light switch.
What are the components of an operon?
- Promoter
- Operator
- Genes
- Regulatory Gene
What is the function of the promoter in an operon?
It is where RNA polymerase binds to start transcription.
What is the role of the operator in an operon?
It controls RNA polymerase’s access.
What does the regulatory gene do in an operon?
It makes a repressor protein that turns the operon ON or OFF.
What is a repressible operon?
Usually ON but can be turned OFF, e.g., Trp Operon.
What is the function of the trp operon?
It makes enzymes to build tryptophan.
When is the trp operon turned OFF?
When too much product (tryptophan) is present.
What is an inducible operon?
Usually OFF but can be turned ON, e.g., Lac Operon.
What is the function of the lac operon?
It makes enzymes to break down lactose.
When is the lac operon turned ON?
When the substrate (lactose) is present.
What is the default state of the repressible operon?
ON.
What is the default state of the inducible operon?
OFF.
How does prokaryotic gene regulation help bacteria?
It helps conserve energy by only making proteins when needed.
TRP Operon
Makes enzymes that help bacteria synthesize tryptophan
Describe the purpose of the trp operon.
The trp operon makes enzymes that help bacteria synthesize tryptophan, an amino acid.
Explain how the trp operon functions when tryptophan levels are low.
When tryptophan levels are low, the trp operon is ON, allowing RNA polymerase to bind to the promoter and transcribe genes to produce tryptophan.
Define the role of tryptophan in the regulation of the trp operon.
Tryptophan acts as a corepressor that binds to a repressor protein, activating it to block RNA polymerase when tryptophan levels are high.
How does the trp operon conserve energy for bacteria?
The trp operon conserves energy by turning OFF when there is enough tryptophan present, preventing unnecessary production of tryptophan.
Summarize the conditions under which the trp operon is ON and OFF.
The trp operon is ON when tryptophan levels are low, allowing tryptophan production, and OFF when tryptophan levels are high, stopping production.
Describe the purpose of the lac operon.
The lac operon makes enzymes that help bacteria break down lactose for energy.
Explain the state of the lac operon when lactose is absent.
The lac operon is normally OFF when lactose is absent, preventing the production of enzymes for lactose breakdown.
How does the presence of lactose affect the lac operon?
The presence of lactose turns the lac operon ON, allowing the production of enzymes to break down lactose.
Summarize the difference between the trp operon and the lac operon.
The trp operon is repressible and turns OFF when tryptophan is abundant, while the lac operon is inducible and turns ON when lactose is present.
Describe the role of a repressor protein in gene transcription.
A repressor protein attaches to the operator, blocking transcription and keeping the genes OFF.
Explain how lactose influences the repressor protein.
Lactose acts as an inducer by binding to the repressor, causing it to change shape and detach from the operator.
How does RNA polymerase become active in the presence of lactose?
When the repressor falls off the operator due to lactose binding, RNA polymerase can bind to the promoter and transcribe the genes.
What is the outcome when lactose is present in the environment?
The operon turns ON, allowing bacteria to break down lactose into glucose and galactose for energy.
Identify the regulatory molecule for the Lac operon.
Lactose acts as an inducer for the Lac operon.
Identify the regulatory molecule for the Trp operon.
Tryptophan acts as a corepressor for the Trp operon.
What regulatory mechanism controls the Lac operon?
The Lac operon is turned ON when lactose is present.
Point Mutations
mutation in one base where a nucleotide is substituted
What are the three main types of point mutations?
- Silent Mutation
- Missense Mutation
- Nonsense Mutation
What is a silent mutation?
The DNA changes, but the amino acid stays the same, resulting in no effect on the organism.
What is a missense mutation?
The DNA changes, and the amino acid also changes, which may affect how the protein functions.
What is a nonsense mutation?
The DNA change causes a STOP codon to appear too early, leading to an incomplete protein, which is usually harmful.
What is a frameshift mutation?
A frameshift mutation occurs when a nucleotide is added or deleted, shifting the entire reading frame of the gene effecting proteins the most
What about frame shift mutations in introns?
it does not affect the protein bc introns are spliced out
How are mutations innherited?
mutations must be in the gametes/sex cells
What are bacteriophages?
Bacteriophages (phages) are viruses that infect bacteria by injecting their genetic material into bacterial cells.
What are the two main life cycles of bacteriophages?
- Lytic Cycle
- Lysogenic Cycle
What is the lytic cycle?
The lytic cycle is when the virus quickly hijacks the bacterial cell, makes many copies of itself, and destroys the host.
What are the steps of the lytic cycle?
1) bacteriophage injects DNA into cell
2) viral DNA will make more bacteriophages
3) once there are a lot of viruses they will lyse the cell and infect others
What is the lysogenic cycle?
The lysogenic cycle is when the virus hides inside the bacterial cell and stays dormant for a long time before becoming active.
What happens during the lysogenic cycle?
1) bacteriophage injects DNA into bacteria
2) DNA is incorporated into host cells DNA
3) bacterial and viral DNA mixed as bacteria replicates, do does the virus DNA (prophage)
What is transformation in bacteria?
Transformation is when bacteria absorb free DNA from their environment.
Where does the free DNA often come from in transformation?
The free DNA often comes from dead bacteria that have lysed (burst open) and released their genetic material.
What happens to the new DNA after it is absorbed by a bacterium in transformation?
The new DNA can integrate into the bacterium’s own genome, giving it new traits.
What are the steps of the transformation process?
- A bacterial cell dies and releases its DNA into the environment.
- A nearby living bacterium takes up a piece of this free DNA.
- If the DNA is useful, it may integrate into the bacterium’s genome through homologous recombination.
- If successful, the bacterium expresses the new genes.
How can transformation contribute to antibiotic resistance?
Transformation is one way some bacteria acquire antibiotic resistance genes.
What is transduction in bacteria?
Transduction is when viruses accidentally transfer DNA (including antibiotic resistance genes) from one bacterium to another.
What type of virus is involved in transduction?
The virus involved is called a bacteriophage (phage) because it infects bacteria.
What are the steps of the transduction process?
- A phage infects a bacterium.
- The phage accidentally takes some bacterial DNA.
- The virus infects a new bacterium.
- The new bacterium gains antibiotic resistance.
What are the 4 ways bacteria can exchange or move genes?
1) transformation
2) transduction
3) conjugation
4) transposons
What is conjugation in bacteria?
Conjugation is a process where bacteria transfer genetic material through direct contact, typically involving a pilus.
What is the role of the pilus in conjugation?
The pilus is a tube-like structure that connects the donor bacterium to the recipient bacterium for DNA transfer.
What is an F+ bacterium?
An F+ bacterium is one that has a special plasmid (F plasmid) that allows it to form a pilus and participate in conjugation.
What happens during the DNA transfer step?
A copy of the F plasmid, which may carry antibiotic resistance genes, is sent through the pilus into the recipient bacterium.
Transposons
aka jumping genes are genes that move from one location to another on a chromosome
What are restriction enzymes?
Restriction enzymes cut DNA at specific sites, creating sticky ends.
What are sticky ends?
Sticky ends are short, single-stranded overhangs that help DNA fragments join together/ where you put complimentary bases
Polymerase Chain Reaction
used to amplify DNA and make multiple copies
Thermal Cycling
heat and cool down the DNA
What is needed to replicate DNA?
nucleotides, primers, TAQ polymerase
TAQ Polymerase
found in bacteria that can withstand high temps
What are the steps of polymerase chain reaction?
1) denature - heat the dna and open it up
2) annealing - cool it down, bring the double strand back together
3) add bases and nucleotides are added to exposed bases
Why is PCR important?
its used to replicate small quantites of DNA
