Podcast
Questions and Answers
What is the primary function of DNA gyrase in prokaryotic genomes?
What is the primary function of DNA gyrase in prokaryotic genomes?
- To degrade double-stranded DNA.
- To reduce supercoiling, facilitating replication and transcription. (correct)
- To form chromatin structures similar to eukaryotes.
- To introduce positive supercoiling, increasing torsional stress.
Which of the following is a key characteristic of prokaryotic genomes compared to eukaryotic genomes regarding DNA structure?
Which of the following is a key characteristic of prokaryotic genomes compared to eukaryotic genomes regarding DNA structure?
- Prokaryotic genomes are typically linear and associated with histones.
- Prokaryotic genomes are circular and form chromatin structures.
- Prokaryotic genomes are circular and supercoiled around a protein core. (correct)
- Prokaryotic genomes contain extensive non-coding regions.
In prokaryotic gene structure, what is the primary role of the promoter region?
In prokaryotic gene structure, what is the primary role of the promoter region?
- Binds the transcription apparatus to initiate transcription. (correct)
- Encodes the protein sequence.
- Binds ribosomes to initiate translation.
- Initiates the termination of transcription.
What is the significance of the -10 and -35 consensus sequences in prokaryotic promoters?
What is the significance of the -10 and -35 consensus sequences in prokaryotic promoters?
How does a single base pair change in the -35 box consensus sequence affect transcription at the transcription start site?
How does a single base pair change in the -35 box consensus sequence affect transcription at the transcription start site?
What is a key function of enhancer sequences in gene regulation?
What is a key function of enhancer sequences in gene regulation?
Which of the following best describes the organization of genes in an operon?
Which of the following best describes the organization of genes in an operon?
What is the functional consequence of genes being arranged into operons?
What is the functional consequence of genes being arranged into operons?
What defines a polycistronic RNA?
What defines a polycistronic RNA?
Which of the following is an advantage of prokaryotes having a smaller genome compared to eukaryotes?
Which of the following is an advantage of prokaryotes having a smaller genome compared to eukaryotes?
What could be considered a disadvantage of a smaller genome?
What could be considered a disadvantage of a smaller genome?
Which feature is commonly found in eukaryotic genomes?
Which feature is commonly found in eukaryotic genomes?
How does the position of a gene on a prokaryotic chromosome affect its protein expression?
How does the position of a gene on a prokaryotic chromosome affect its protein expression?
What is the primary role of the Termination site (dif) in a prokaryotic genome?
What is the primary role of the Termination site (dif) in a prokaryotic genome?
During transcription, what does the promoter region in eukaryotes do?
During transcription, what does the promoter region in eukaryotes do?
What makes some eukaryotic so large?
What makes some eukaryotic so large?
What is true about the consensus sequence?
What is true about the consensus sequence?
Based on the diagram, what is the main difference between the genome of bacteria compared to mammals?
Based on the diagram, what is the main difference between the genome of bacteria compared to mammals?
In the central dogma of molecular biology, what determines the function of a gene?
In the central dogma of molecular biology, what determines the function of a gene?
Why are prokaryotes good model organisms?
Why are prokaryotes good model organisms?
According to the definition, which of the following contains TSS?
According to the definition, which of the following contains TSS?
What is meant by gene expression?
What is meant by gene expression?
What is the transcription start site?
What is the transcription start site?
Which mechanism contributes directly to controlling levels of protein?
Which mechanism contributes directly to controlling levels of protein?
Which of the two strands encode genes in prokaryotes?
Which of the two strands encode genes in prokaryotes?
What helps reduce supercoiling to allow replication and transcription?
What helps reduce supercoiling to allow replication and transcription?
What kind of genomes are prokayotic?
What kind of genomes are prokayotic?
Why does the circularised structure of prokayotic genomes reduce torsional stress?
Why does the circularised structure of prokayotic genomes reduce torsional stress?
What are the two main consensus sequences?
What are the two main consensus sequences?
What does non-coding DNA refer to?
What does non-coding DNA refer to?
Rather than forming chromatin, the circularised structure promotes the formation of a ______ structure, which reduces torsional stress.
Rather than forming chromatin, the circularised structure promotes the formation of a ______ structure, which reduces torsional stress.
In prokaryotes, the formation of a supercoiled structure, rather than chromatin, diminishes the ______ stress on the molecule.
In prokaryotes, the formation of a supercoiled structure, rather than chromatin, diminishes the ______ stress on the molecule.
______ can facilitate the reduction of supercoiling in prokaryotes, aiding in replication and transcription processes.
______ can facilitate the reduction of supercoiling in prokaryotes, aiding in replication and transcription processes.
A ______ sequence comprises the nucleotides most frequently found at a specific location in DNA.
A ______ sequence comprises the nucleotides most frequently found at a specific location in DNA.
The ______ is the DNA sequence to which transcription apparatus binds to initiate transcription and indicates strand direction.
The ______ is the DNA sequence to which transcription apparatus binds to initiate transcription and indicates strand direction.
The first DNA nucleotide that is transcribed into RNA is called the ______.
The first DNA nucleotide that is transcribed into RNA is called the ______.
The shape of the DNA at the promoter and in the first ~50bp of the first gene will affect what happens at the ______.
The shape of the DNA at the promoter and in the first ~50bp of the first gene will affect what happens at the ______.
______ fine-tunes recognition of a specific sequence, influencing protein binding to DNA.
______ fine-tunes recognition of a specific sequence, influencing protein binding to DNA.
Changes to the shape of either the DNA or the protein can alter the ______ of binding between them.
Changes to the shape of either the DNA or the protein can alter the ______ of binding between them.
In prokaryotes, the position of a gene on the ______ significantly affects the level of protein expression.
In prokaryotes, the position of a gene on the ______ significantly affects the level of protein expression.
The location of the ______ is opposite the origin of replication in a prokaryotic genome.
The location of the ______ is opposite the origin of replication in a prokaryotic genome.
The lactose (or lac) ______ is a cluster of genes that control disaccharide metabolism to glucose and galactose.
The lactose (or lac) ______ is a cluster of genes that control disaccharide metabolism to glucose and galactose.
______ are structures where a number of genes are located next to one another on the genome.
______ are structures where a number of genes are located next to one another on the genome.
DNA or RNA that is not translated into protein is referred to as ______.
DNA or RNA that is not translated into protein is referred to as ______.
A single mRNA that is generated from multiple genes is known as ______.
A single mRNA that is generated from multiple genes is known as ______.
A change in the single base pair in the -35 box can prevent ______.
A change in the single base pair in the -35 box can prevent ______.
The DNA of prokaryotes are ______ stranded.
The DNA of prokaryotes are ______ stranded.
______ sequences are regulatory DNA sequences that enhance the transcription of an associated gene.
______ sequences are regulatory DNA sequences that enhance the transcription of an associated gene.
[Blank] is the process of turning what is encoded in a gene into a function.
[Blank] is the process of turning what is encoded in a gene into a function.
When studying what affects the binding of proteins to DNA, it relates to ______ principles.
When studying what affects the binding of proteins to DNA, it relates to ______ principles.
The ______ has a fast replication cycle, making it a good model organism.
The ______ has a fast replication cycle, making it a good model organism.
Proteins control the processes of ______ in weeks 5-7 of the module.
Proteins control the processes of ______ in weeks 5-7 of the module.
Knowing the gene stucture leads to understanding the scale of the task of ______ in week 5 of the module.
Knowing the gene stucture leads to understanding the scale of the task of ______ in week 5 of the module.
An advantage of prokaryotes compared to eukaryotes is their ______ gene structure.
An advantage of prokaryotes compared to eukaryotes is their ______ gene structure.
Proteins moving into the nuecleus to bind to specific sequences are ______.
Proteins moving into the nuecleus to bind to specific sequences are ______.
The main 2 of the ______ includes the pribnow box.
The main 2 of the ______ includes the pribnow box.
[Blank] is an objective of the learning to label the diagram showing the regions of a gene for both eukaryotes and prokaryotes.
[Blank] is an objective of the learning to label the diagram showing the regions of a gene for both eukaryotes and prokaryotes.
It is an objective to explain the advantages and ______ of having a smaller genome and compare this with to those of having a larger genome.
It is an objective to explain the advantages and ______ of having a smaller genome and compare this with to those of having a larger genome.
The shape of the DNA depends on ______ interactions.
The shape of the DNA depends on ______ interactions.
The position of the gene on the ______ direction affects the level of protein expression.
The position of the gene on the ______ direction affects the level of protein expression.
Flashcards
Promoter
Promoter
DNA sequence where transcription starts, indicating direction and strand. Also contains TSS.
Transcription Start Site (TSS)
Transcription Start Site (TSS)
The first DNA nucleotide that is transcribed into RNA.
Consensus Sequence
Consensus Sequence
Most common nucleotides at a specific DNA location.
Prokaryotic Genome Structure
Prokaryotic Genome Structure
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Operons
Operons
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Polycistronic mRNA
Polycistronic mRNA
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Non-coding DNA
Non-coding DNA
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Gene Expression
Gene Expression
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Enhancer
Enhancer
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Transcription Factors
Transcription Factors
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Promoter Definition
Promoter Definition
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Prokaryotic Genome coding
Prokaryotic Genome coding
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What is Polycistronic.
What is Polycistronic.
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What is Prokaryotic genome structure
What is Prokaryotic genome structure
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DNA shape for binding?
DNA shape for binding?
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What are operons?
What are operons?
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Transcription Start Site
Transcription Start Site
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Prokaryotic Genome Coding
Prokaryotic Genome Coding
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Study Notes
- My Surrey Attendance code: CD-PF-WB
- Gene and genome structures
- Student consultation and feedback hour
- Week 2: Friday 14th February 13.30-14.30
- Week 3: Thursday 20th February 12.00-13.00
- Book an appointment
Learning Objectives
- Label the regions of a gene for both eukaryotes and prokaryotes in a diagram.
- Describe non-coding DNA in prokaryotes
- Explain the advantages and disadvantages of having a smaller genome compared to a larger genome
- Describe the assembly and rough structure of prokaryotic genomes
Number of Genes
- Guess how many genes there are in prokaryotic and eukaryotic genomes.
- Guess how many base pairs there are in a gene in prokaryotic and eukaryotic genomes.
Prokaryotic vs Eukaryotic Genomes
- Prokaryotes have mostly coding DNA
- Eukaryotes have mostly non-coding DNA
- Number of nucleotide pairs per haploid genome is larger in eukaryotes
Prokaryotic Genome Structure
- A prokaryotic genome is circularized double stranded DNA
- Forms a supercoiled structure instead of chromatin, reducing torsional stress.
- DNA gyrase and a protein core helps reduce supercoiling for replication and transcription.
- Brown, T.A. (2002) Genomes 2nd Edition Figures 2.17 and 2.18
Anatomy of a Gene
- Complete the labels for prokaryotic genes
- Enhancers: Structural support to bring proteins close to the RNA polymerase to bind to the promoter, to initiate transcription.
- GTACCCATA
- Provides structural support to bring proteins close to the RNA polymerase to make sure that it binds to the promoter, to initiate transcription
- TTGACA TATAAT provides gene A, gene B and gene C
- What is in the Promoter?
- RNA polymerase binds to the promoter
- Dictates transcription start and strand, contains -10 and -35 consensus sequences
- Transcription start site and other sequences recruit proteins to assist in transcription initiation
- Alberts 6th Ed: Fig 6-12a & 13
Definitions
- Promoter definition: DNA sequence to which transcription apparatus binds to initiate transcription; indicates direction and contains TSS
- TSS definition: The first DNA nucleotide that is transcribed into RNA.
- Consensus sequence definition: The sequence that comprises the most commonly encountered nucleotides found at a specific location in the DNA.
Transcription sites
- RNA polymerase and DNA in the promoter interact
- Interaction depends on:
- Consensus sequence (-35 box change can prevent binding).
- The shape of the DNA at promoter and in the first ~50bp of the first gene.
- Alberts 6th Ed: Fig 6-12a & 13
DNA Binding
- Protein interface must match the shape of the DNA
- Enables electrostatic interactions
- Fine tunes recognition of specific sequence
- Changes in shape of DNA or protein affect binding strength
- Alberts 6th Ed: Fig 7-9a
Prokaryotic Genome
- Both strands encode genes
- High coding sequence
- Gene position on chromosome affects protein expression.
- Termination site (dif) location is opposite the origin of replication (Ori)
- Features non-structured regions
- Bryant JA et al. (2014) Nucleic Acids Res 42(18):11383-92
Genes and Operons
- Operons have multiple genes located next to each other on the genome
- Genes are under a single promoter and expressed as one polycistronic RNA unit.
- Genes control a process, the lac operon has 3 genes that control disaccharide metabolism to glucose and galactose.
- Under control of a single promoter and expressed under a polycistronic RNA
Eukaryotes
- Complete labels for Eukaryotic genes.
- Eukaryotic genomes tend to be larger
Gene Expression
- Generating protein = gene expression
- Protein levels are controlled by:
- Rate of transcription
- Rate of mRNA degradation
- Rate of protein synthesis
- Rate of protein degradation
- Alberts 6th Ed: Fig 6-3
Prokaryotes as Model Organisms
- Fast replication cycle
- Simple gene structure
- Simple gene regulation (operon)
- It is faster to see changes and easier to cause some changes and see the effects that it has on protein structure, function and organismal survival
Linking to Rest of Module
- Knowing gene/genome structure will:
- Create understanding of replication scale (week 5)
- Demonstrate information inheritance in large molecules
- Understand use of other species regulatory processes
- Emphasize proteins control replication, transcription, translation, activity, expression and localisation (weeks 5-7)
Glossary
- Consensus sequence: the most commonly encountered nucleotides found at a specific location in the DNA. 2 main ones are pribnow box (10bp upstream of the TSS) and -35 sequence (35bp upstream of the TSS).
- Non-coding: DNA or RNA that is not translated into protein.
- Polycistronic: a single mRNA (generated from multiple genes) generates multiple proteins.
- Promoter: DNA sequence to which transcription apparatus binds to initiate transcription; indicates direction and which strand of the DNA elongation occurs on, also contains TSS. Transcription start site (TSS): The first DNA nucleotide that is transcribed into RNA.
- Transcription factors: proteins that move into the nucleus to bind to specific sequences (response elements) and recruit additional proteins to stimulate transcription.
- Enhancer: Enhancer sequences are regulatory DNA sequences that, when bound by specific proteins called transcription factors, enhance the transcription of an associated gene.
- Gene Expression: The process of turning what is encoded in a gene into a function. As the central dogma is applied this means that this occurs through transcription of RNA molecules, coding for proteins (or non-coding RNA).
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