Gene Expression Flashcards
Genome
All the genetic material in the chromosomes of an organism, including its genes and DNA sequences.
Coding and non-coding DNA
The DNA that comprises chromosomes (and on a smaller scale: genes) is often classified as either coding DNA or non-coding DNA.
Coding DNA
DNA that is both transcribed and translated (eg. the exon component of genes).
Non-coding DNA
DNA that is not both transcribed and translated. The function of much of the non-coding DNA is unknown. Non-coding DNA has many gene regulatory functions and species complexity probably lies in the non-coding sections of the genome rather than the coding sections. So, it plays an important role in a cell’s survival.
Major categories of non-coding DNA
Structural DNA
DNA sequences coding for Functional non-coding RNA
Introns
Regulatory DNA sequences
Structural DNA
eg. centromeres and telomeres which are not transcribed (are composed of repeating nucleotide sequences). This DNA helps to maintain the structure of chromosomes. (See the image below left)
DNA sequences coding for Functional non-coding RNA
eg. tRNA and rRNA which are transcribed but not translated (are made from DNA and move to cytoplasm)
Introns
DNA sections within genes - are transcribed but RNA copies are removed before mature mRNA leaves the nucleus ie. before translation.
Regulatory DNA sequences
eg. promotors, operator and enhancer sequences which influence the process of transcription
Protein Synthesis
Genes are mainly expressed via their DNA sequence being used to make a functional gene product. Functional gene products are either:
proteins (made via protein synthesis)
functional noncoding RNA (eg. tRNA or rRNA molecules which are used in protein synthesis).
Main molecules involved in protein synthesis
DNA and RNA (made of nucleotides).The other important type of molecule is protein (made of amino acids).
A triplet
three consecutive bases in DNA (eg. template strand)
A codon
three consecutive bases in mRNA
An anti-codon
three consecutive bases in a particular part of tRNA
Protein synthesis in eukaryotic cells
Transcription occurs in the nucleus and Translation in the cytoplasm at the ribosomes
Transcription occurs before Translation (pre-mRNA is modified in between)
Eukaryotic DNA does have introns.
Protein synthesis in prokaryotic cells
Both transcription and translation occur in the cytoplasm / cytosol (as their is no nucleus).
free floating ribosomes can attach to mRNA as it forms. Thus, translation and transcription occur at the same time.
prokaryotic DNA has no introns. Thus pre-mRNA modification does not need to occur.
Major steps of protein synthesis
- Transcription
Occurs in the nucleus
DNA base sequence in genes is a template that is copied into a form that can leave the nucleus (mRNA). - Pre- mRNA processing
Occurs in the nucleus
Pre mRNA is modified to become mature RNA which leaves the nucleus. (Non-coding INTRONS are removed from the mRNA and coding EXONS are spliced back together. A 5’cap and a 3’polyA tail are also added to the ends of the mRNA) The modified mRNA is now called mature mRNA)(Remember: Exons are are expressed and are expelled from the nucleus while Introns go into the trash) - Translation
Occurs in the cytoplasm (at the ribosomes)
The mature mRNA is decoded by ribosomes and used to direct the sequence of amino acids in a polypeptide chain.
Transcription
- Initiation- RNA polymerase binds to a promotor region upstream of the gene. The DNA unzips (H bonds break) as a result of enzyme action.
- Elongation- One side (Template strand) of a genes DNA is used as a recipe for making a mRNA strand. (Note the strand complimentary to the template strand is called the Coding strand).
Free floating RNA nucleotides are attracted to their complimentary exposed DNA bases (each three bases in the DNA sequence is called a triplet) and bond together (with the help of the enzyme called RNA polymerase) to form a single sided RNA chain. (Note: mRNA is always synthesised in a 5’ to 3’ direction)
- Termination- RNA polymerase reaches a terminator region at the end of the gene and transcription ends.The DNA double helix reforms.
This initial messenger RNA (pre-mRNA) chain then breaks away from the original DNA template and is modified in three ways before it leaves the nucleus (see mRNA modification below).
Pre- mRNA processing
1.- a 5’ cap is added to one end of the mRNA (thought to allow mRNA to attach to ribosomes)
- a 3’ poly A tail is added to the other end of the mRNA (thought to allow the final mRNA to leave via nuclear pores)
- introns (non coding regions of the mRNA) are removed and exons (coding regions) are spliced back together making the final / mature mRNA that goes to the ribosomes shorter.
Translation
- Initiation- The modified final mRNA attaches to a ribosome (made of rRNA) and starts to be ‘decoded’ three bases (a codon) at a time. When the sequence AUG (the start codon) is ‘read’ by the ribosome then translation will begin.
Each codon codes for a specific amino acid (see the mRNA – amino acid table below or on pg 79 of your IB Biology Biozone workbook…showing 61 codons coding for approx. 20 amino acids)
- Elongation- Specific amino acids are brought to the ribosomes (by transfer RNA (tRNA) molecules). tRNA molecules have anticodons at their base which temporarily bond to the mRNA codons ( as they are complimentary) at the ribosome. Adjacent amino acids then bond together (via peptide bonds) to form a polypeptide chain.
tRNA decodes mRNA sequences by matching amino acids to codons of the mRNA
The tRNA molecules move back to the cytoplasm to be ‘recharged’ (pick up new amino acids).
- Termination- Translation ends after the ribosome reads a stop codon (either UAA, UAG or UGA). Stop codons do not code for amino acids (have no corresponding tRNA molecules). The polypeptide chain is released from the ribosome.
Structural genes
Code for proteins and RNA’s that are not regulatory in nature eg. enzymes, hormones, membrane proteins, cytoskeleton proteins, rRNA or tRNA molecules.
Regulatory genes
Code for transcription factor proteins that are regulatory in nature
Transcription factor proteins (TFP)
DNA binding proteins.
They bind to either the promotor, operator, enhancer or silencer regions of DNA (which are often located upstream of a structural gene).
Transcription factor proteins regulate transcription by influencing whether an enzyme called RNA polymerase can attach to the promotor region of DNA and then initiate transcription.
Two major categories of Transcription factor proteins are:
Activator proteins
Repressor proteins
Activator proteins
Bind to enhancer DNA sequences and switch transcription ‘on’ (up regulate structural gene expression).
Repressor proteins
Bind to silencer DNA sequences and switch transcription ‘off’ (down regulate structural gene expression).
Controlling gene expression in eukaryotic organisms
It usually involves an enhancer region of DNA (located a fair distance upstream of a structural gene) folding back over and interacting with the promotor region near the structural gene. Transcription factors bind to promotor regions which enable RNA polymerase to bind here and initiate transcription.
The enhancer region is a short regulatory sequence of DNA that works to enhance or speed up the rate of transcription.
The promoter region is a length of DNA to which the RNA polymerase enzyme binds to initiate transcription (mRNA nucleotides being sequenced together using the DNA template).
Controlling gene expression in prokaryotic organisms
The regulation of genes often involves operons.
An operon is a length of DNA made up of structural genes and control sites (eg. operator and promotor regions, which are located ‘upstream on 5’ side’ of the structural genes).
The operator region is a regulatory DNA sequence that can act as a ‘switch’ and turn a gene on or off.
The promoter region is a length of DNA to which the RNA polymerase enzyme binds to initiate transcription.
In prokaryotic organisms regulatory genes, often found upstream of the operon, can make repressor proteins that bind to the operator region (only found in prokaryotic cells) and supress gene expression by preventing RNA polymerase binding to the adjacent promotor region.
Regulatory mechanisms
Regulatory genes code for proteins called transcription factors that bind to regulatory DNA sequences (eg. ‘promotor’ regions, enhancers or silencers) upstream of structural genes. Transcription factors can either ‘up regulate’ (enhance) or ‘down regulate’ (supress) the transcription of a structural gene.
Environmental factors can influence the addition of chemical tags (eg. methylation or acetylation) which influences the coiling of DNA and also transcription. (NOTE: Tightly coiled and highly methylated regions of DNA seem to be transcribed less).
microRNA molecules can be produced from non-coding regions of DNA which influence translation at ribosomes.
The use of chemical tags or microRNA in gene regulation is sometimes also referred to as Epigenetics.
Cell Differentiation associated with Sex determination
On the Y chromosome there is a gene called the Sex Determining Region Y (SRY) gene. This gene produces a transcription factor (SRY) protein that upregulates the production of other transcription factors (eg. SOX 9) triggering the embryonic gonad tissue/ cells to differentiate and the gonad becomes a testis (seminiferous tubules develop and testosterone production begins). When no SRY protein is made, low SOX9 concentrations will not stimulate testis production so the embryonic gonad remains in the female form.
Morphological development
Body plan genes (the genes that control the development of body plans) are similar in plants, animals and fungi.
The HOX genes are types of Homeotic (Homeobox) genes which are a collection of similar genes that are expressed in particular patterns at particular stages of development. They produce specific protein transcription factors. In animals, HOX genes control events such as the embryonic development of a head to tail axis, segmentation and the development of appendages/ limbs. Eg. HOX genes in insects specify which appendage grows from which body segment.
Epigenetics
Any mechanism that alters gene expression without altering the DNA sequence. The epigenome refers to a system of gene control outside of the DNA (‘above the genome’) .
Epigenetic inheritance
Involves the inheritance of traits transmitted by mechanisms not directly involving the DNA nucleotide sequence.
Chemical Tags (affecting transcription)
Example of an epigenetic process.
Histone modification: how tightly coiled the DNA is around histones (and also how tightly packed nucleosomes are) is influenced by the presence or absence of specific chemical tags.
DNA acetylation -acetyl groups are added to DNA which ‘relaxes’ histone structures and enhances transcription
DNA methylation- the addition of methyl groups to the DNA at the start of a structural gene and will often reduce transcription.
Influence gene expression via enhancing or suppressing transcription.
microRNA production (affecting translation)
Example of an epigenetic process.
Some small RNA sequences (approx. 22 nucleotides long) that can silence genes by either degrading mRNA or blocking translation at ribosomes.
These microRNA molecules can interfere with protein synthesis by stopping translation (by attaching to mRNA and either blocking mRNA from being translated by ribosomes or by degrading mRNA).
RNA bases
AUGC
DNA bases
ATGC
Messenger RNA (mRNA)
A copy of the genetic code made from DNA in a single sided form, whose codons (3 base sequences) can be read and are used to make proteins. It carries the genetic information from the nucleus (via nuclear pores) to the ribosomes in the cytoplasm of the cell.
Ribosomal RNA (rRNA)
It is located in the cytoplasm of the cell, ribosomes are made up of ribosomal RNA. The ribosome exists as two subunits (a large and a small subunit). It directs the translation of mRNA into proteins which sits between the two subunits during translation.
Transfer RNA (tRNA)
It is located in the cytoplasm of the cell. It brings (transfers) amino acids to ribosomes during translation. It contains an anticodon that is complimentary to a three nucleotide codon of mRNA that is being decoded at the ribosome. The amino acids carried by tRNA can then be joined together and processed to make a polypeptide chain and proteins.
DNA –> Protein
DNA
Transcription
RNA
Translation
Protein
