Lecture 9: Gene To Protein Flashcards
What is gene expression?
The process of going from DNA to a functional product.
The Central Dogma
DNA -> RNA -> Protein
What are the DNA and mRNA bases?
Adenine, Guanine, Thymine, Cytosine and Uracil.
Uracil is easier to make than Thymine.
Thymine is more stable -> DNA is the inherited material hence needs to be more stable
A-T/U
C-G
What is the genotype?
An organism’s hereditary information.
What is the phenotype?
Actual observable or physiological traits.
How do genotype and environment interact?
They determine our phenotype.
What is DNA?
Deoxyribonucleic acid, the heritable material that stores and transmits information.
What is RNA?
Ribonucleic acid, which acts as a messenger to make proteins from DNA information.
What are the three main steps of protein synthesis?
Transcription of RNA from DNA
Processing of pre-mRNA to mature mRNA
Translation of mRNA to protein
What occurs during transcription?
RNA is synthesized from a DNA template.
What are the three phases of Transcription?
Initiation -> polymerase binds to promoter
Elongation -> moves downstream through the gene, transcribing RNA
Termination -> detaches after terminator reached
What is the role of RNA polymerase during transcription?
It binds to the promoter region along with other transcription factors to form the transcription initiation complex and synthesizes RNA.
Why is it called the 3’ or 5’ ends?
Due to phosphate group connecting to the 3’ or 5’ carbon
What is the TATA box?
A sequence of DNA found in the promoter region which marks where transcription should be initiated
The typical promoter element ~25nt upstream of the transcription start site.
What is TBP?
TATA box binding protein is a transcription factor that binds to the TATA box of the promoter region forming transcription initiation complex.
What is the role of transcription factors?
They are required for the assembly of the transcription initiation complex.
What is the process of initiation in transcription?
Initiation is the assembly of proteins required before transcription can commence
Eukaryotic Primer - DNA contains a promoter region in which the TATA box can be found
Several Transcription factors bind to promoter region - Assembly of several transcription factors including the TATA box binding protein (TBP)
Transcription initiation complex - This changes the shape of the promoter, RNA Polymerase II can now bind along with more transcription factors to form the transcription initiation complex
What is the polyadenylation signal?
A sequence of nucleotide bases that signal the termination of transcription hence the release of pre-mRNA and RNA polymerase
What is the process of elongation in transcription?
10-20 nucleotides exposed at a time when DNA unwound, allowing RNA
Nucleotides to come in and bond to their basepair. Producing a phosphodiester bond (strong) between the RNA nucleotides
Moves downstream through the gene, transcribing RNA
Complementary RNA nucleotides added to 3’ end of growing transcript (3’OH of transcript binds with 5’ phosphate of incoming nucleotide)
Double helix reforms as transcript leaves the template strand
What is the process of termination in transcription?
Detaches after terminator reached after transcription of the polyadenylation signal (AAUAAA) nuclear enzymes release the pre-mRNA and RNA polymerase then dissociates from the DNA
The polyadenylation signal (AAUAAA) indicates where transcription ends.
What are the 3 steps to processing stage of gene expression?
Capping, tailing, splicing
What is capping in mRNA processing? Why?
A modified guanine nucleotide is added to the 5’ end.
Capping and tailing are thought to facilitate export, confer stability and facilitate ribosome binding in cytoplasm
RNA rapidly degrades
What is tailing in mRNA processing? Why?
50-250 adenine nucleotides (polyA) are added to the 3’ end.
Capping and tailing are thought to facilitate export, confer stability and facilitate ribosome binding in cytoplasm
RNA rapidly degrades
What are exons?
Regions that remain in mature RNA.
What are introns?
Intervening regions that do not remain in mature RNA.
What are UTRs?
Untranslated regions at 5’ and 3’ ends of mRNA
What is splicing?
Introns are removed from the transcript
What is a spliceosome?
A large complex of proteins and small RNAs, removes introns and joins exons to form mature mRNA.
What is alternative splicing?
A process that allows different combinations of exons to produce multiple mRNA forms.
Why do we have alternative splicing/introns?
Larger organisms have introns, allowing for much higher complexity and variation
Alternative splicing allows for multiple gene products from the same gene
~20,000 genes, there could be many times that number of proteins!!
What are codons?
Groups of three mRNA bases in a row that code for a specific amino acid
What is the relationship between codons and amino acids?
Codons are translated into amino acids during protein synthesis.
What is the role of tRNA in translation?
tRNA molecules within the cytosol with specific anticodons carry corresponding amino acids to the ribosome and matches them to the mRNA codons.
What are the three sites in the ribosome?
- A site (Aminoacyl-tRNA binding site)
- P site (Peptidyl-tRNA binding site)
- E site (Exit site)
How do amino acids connect to growing polypeptide chain?
The amino acid is added via peptide bonds to the growing polypeptide chain
What initiates translation?
The small ribosomal subunit with the initiator tRNA already attached binds with mRNA and scans for the start codon (AUG).
What is tRNA’s function?
tRNA is the physical link between the mRNA and the amino acid sequence of proteins
What is required for the assembly of the translation initiation complex?
Energy in the form of GTP (Guanosine triphosphate)
What happens during elongation in translation?
tRNA recognizes codon, tRNA translocates from A to P site.
The large subunit of the ribosome catalyses peptide bond formation, removes it from tRNA in P site
tRNA in P site moves to E and is released
Energy is required (GTP)
What signals termination in translation?
Recognition of a stop codon (UAG, UAA, UGA) in the A site by a release factor
Release factor promotes hydrolysis
Bond between p-site tRNA and last amino acid is hydrolyzed, releasing polypeptide chain
Ribosomal subunits and other components dissociate
Hydrolysis of two GTP molecules required
What are the control points of Gene to Protein?
Transcription factors need to assemble, and DNA needs to be accessible
Capping, extent of polyadenylation, alternate splicing, producing an mRNA able to be translated specific proteins assist in nuclear export of mRNA regulatory proteins can block translation, variable mRNA life-spans
What is the importance of gene expression regulation?
To achieve the right function at the right time and place (temporal and spatial control)
What are housekeeping proteins?
Proteins that are continuously produced
* protein and mRNA are present in large quantities (e.g. Tubulin)
* typically, have longer “half life” in cells
What are temporary proteins?
Produced by cell signaling (e.g. ligand binding a cell surface receptor, or activating an intracellular receptor)
Signal transduced and may enter nucleus to activate transcription
Results in the production of a short-lived protein to carry out the required function
What are the properties of an Animo acid?
Has a Amino group, and Carboxyl group, and a side chain.
The side chains (R groups) determine the properties of each amino acid
What are signal peptides?
Short sequences that direct ribosomes to the endoplasmic reticulum.
What is post-translational modification?
Chemical changes to a protein after translation that can affect its activity.
What are some common post-translational modifications?
- Phosphorylation
- Methylation
- Acetylation
- Biotinylation
- Carboxylation
- Carbohydrate addition
- Cleavage
- Ubiquitination
What is the primary structure of a protein?
The sequence of amino acids determined by DNA.
What forms secondary structure in proteins?
Hydrogen bonds forming alpha helices and beta sheets.
What stabilizes tertiary structure in proteins?
Interactions between side chains (R groups).
What characterizes quaternary structure?
Multiple proteins associating together to form a functional protein.
Not all proteins form quaternary structures
What are the terminus ends of the primary structure?
N – Terminus is the amino end (5’)
C – Terminus is the carboxyl end (3’)
Where does Transcription and Processing occur?
Nucleus
Where does Translation occur?
Cytosol
