Lecture 1 Gene and genome structures Flashcards
Learning Objectives
➢Label a diagram showing the regions of a gene for both eukaryotes and prokaryotes.
➢Describe what non-coding DNA is present in prokaryotes
➢Explain the advantages and disadvantages of having a smaller genome and compare this with to those of having a larger genome.
➢Describe the assembly and rough structure or prokaryotic genome
What a prokaryotic genome looks like
➢Circularised double stranded DNA
➢Rather than forming chromatin the circularised structure promotes the formation of a supercoiled structure. The formation of these reduces the torsional stress on the molecule.
➢This forms around a protein core and DNA gyrase can help reduce supercoiling to allow replication and transcription
what are Enhancers?
Provide structural support to bring proteins close to the RNA polymerase to make sure that it binds to the promoter, to initiate transcription
What is in the promoter?
Dictates where transcription starts and in which direction & which strand.
This is the place that RNA polymerase binds to.
Contains -10 and -35 consensus sequences, transcription start site and other sequences that recruit proteins able to assist in the control of initiation of transcription
Definitions of Promoter, TSS and consensus sequence
Promoter: DNA sequence to which transcription apparatus binds so as toinitiate transcription; it 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.
Consensus sequence: The sequence that comprises the most commonly encountered nucleotides found at a specific location in the DNA
What happens at the transcription start site?
RNA polymerase and the DNA in the promoter interact with one another.
The interaction depends on:
Consensus sequence (a single base pair change in the -35 box can prevent binding).
The shape of the DNA at the promoter and in the first ~50bp of the first gene
why must Protein interface match the DNA shape
✓Enables electrostatic interactions
✓Fine tunes recognition of a specific sequence.
✓Changes to shape of either the DNA or the protein can affect the strength of binding.
What does a prokaryotic genome looks like
➢Both strands encode genes
➢High degree of sequence that codes for proteins.
➢The position of the gene on the chromosome directly affects the level of protein expression.
➢Location of Termination site (dif) is opposite the origin of replication (Ori)
how are Genes arranged into Operons
Operonsare structures where a number ofgenes are located next to one another on the genome.
The genes are under the control of a single promoter and expressed as one unit, known as a poly-cistronicRNA.
Often these genes control a process e.gthe lactose (or lac) operon is composed of 3 genes which control disaccharide metabolism to glucose and galactose
why does Generating protein = gene expression
Levels of protein controlled by:
➢Rate of transcription
➢Rate of mRNA degradation
➢Rate of protein synthesis
➢Rate of protein degradation
what are The benefits of studying prokaryotes as a model organism
➢Fast replication cycle
➢Simple gene structure
➢More simplistic gene regulation (operon)
Therefore, its 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 this to the rest of the module
Knowing the structure of genes and the genome will:
-Create an understanding of the scale of the task of replication (week 5)
-Demonstrate how information is inherited in a large molecule, with potential for mistakes that drive evolution (week 2).
-Understand why we can use other species as a “test” subject or to predict how organisms/species regulate a process (end of the module)
-That proteins control processes of replication, transcription and translation, therefore their activity, expression and localisation are key (weeks 5-7)
Glossary
Consensus sequence: sequence that comprises 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 so as toinitiate transcription; it 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)
Guess how many genes there are in:
Prokaryotic genomes
=Generally small. Some prokaryotic genomes have as few as 150 genes, whereas some have almost 1000 gene
Eukaryotic genomes
=Much larger. Some are almost the same size as large prokaryotic genomes, made up of just a few thousand genes (e.g. some yeasts) whereas some genomes are much larger, in the region of 30,000 genes
Guess how many base pairs are there in a gene in
Prokaryotic genomes
-There is a wide spread but generally smaller. Prokaryotic genomes have as few as 700 base pairs (bp), whereas some have almost genomes of around 10 million (1x107) bp. Each gene has around a few hundred base pairs though
Eukaryotic genomes
-Much larger genome, but its not a linear relationship with prokaryotes due to the non-coding DNA. The smallest eukaryotic genomes are as small ask 600, the human genome sits somewhere in the middle at around 3.5 billion bp whereas some genomes are much larger (bony fish) in the region of 130 billion bp! This means genes are a lot larger, we will come onto quite how much non-coding DNA there is later on
