(bio) Unit 3 - Transcription an Translation Flashcards
Describe central dogma (3 steps)
- DNA replication (information and storage)
- RNA synthesis from DNA strand (information and carrier)
- Protein synthesis aka translation (Active cell machinery)
Difference between RNA and DNA
RNA - OH group on 2nd carbon (only uracil)
DNA - No OH group on 2nd carbon (only thymine)
What carbons are attached to what molecules to form nucleic acids?
Carbon 1: attached to base
Carbon 3: attached to phosphate
In what direction do nucleic acids grow? What direction does newly formed RNA travel along template strand?
- Nucleic acids grow in 5’ to 3’ direction
- Moves along 3’ to 5’ of template strand
What strand is DNA transcribed from
Template strand (non coding)
What bonds hold nucleic acids together?
Phosphodiester bonds (between phosphate groups) and hydrogen bonds (between bases)
Role of mRNA, tRNA, rRNA ?
mRNA: code for proteins
tRNA: adapters between mRNA and amino acids during protein synthesis
rRNA: involved during translation
What subunits does PROKARYOTIC RNA polymerase consist of? What are the functions of these subunits?
subunits sigma factor and core enzyme makes up the entire core enzyme aka holoenzyme.
These subunits synthesize the RNA based on template
Where does the prokaryotic RNA polymerase need to start polymerizing? What does this? Why does sigma need to bind to this?
sigma factor does this by recognizing promotor sequence (regions on non-template strand) and binds to it, located upstream of start of the gene.
Sigma needs to bind to this to properly orient the RNA polymerase holoenzyme for transcription at start site.
What are the two key regions of the prokaryotic promoters sequence.
-10 box and -35 box that will be identified by sigma
(10 and 35 bases upstream from start site)
How does sigma work during Initiation and elongation of transcription in bacteria
- sigma opens the helix
- allows ribonucleoside triphosphate (NTPs) to enter active site and begin transcription
- sigma factor is released once transcription in bacteria begins , only gets things starting correctly
How does termination of transcription in bacteria (prokaryotes) work?
- The sequence reaches a termination signal in DNA template
- The sequence will remove itself from the RNA polyermase and create a hairpin strucutre.
What makes eukaryotic DNA structure different from prokaryotic DNA
Eukaryotes DNA molecules combine with proteins to adopt higher order strucutre - chromatin which consists of DNA strand wrapped in histone proteins
What is the difference between prokaryotes and eukaryotes in terms of types of RNA Polymerases
Eukaryotes have 3 RNA polymerase (but it is focused on RNA polymerase II) - consists of a large team of accessory proteins called general transcription factors
Prokaryotes have 1 RNA polymerase and it consists of a sigma factor
What is the difference between prokaryotes and eukaryotes in terms of promoter sequences?
Eukaryotes have many promoters, an example is the TATA box within the promoter (30 bp upstream)
Prokaryotes have -10 and -35 box
Describe the initiation of transcription in eukaryotes
A TATA box is recognized by the TATA binding protein (TBP) which is a subunit of TFIID.
Binding of the TFIID distorts the helix at the transcription starting point and allows similar structures (TBP’s) to pile on to form transcription initiation complex.
Transcription factors comes off (TFIID stays) once the DNA starts transcription
What is the difference between the mRNA processing of eukaryotes and prokaryotes at the end of transcription?
Eukaryotes: mRNA undergoes a lot of processing before being shipped out of nucleus
- modifications to the transcripts carried out by sources associated with the phosphorylated tail of RNA polymermase II
- capping, splicing, poly A tail (polyadenylation)
Prokaryotes: not in the nucleus
mRNA Capping and Polyadenylation… Where are each modifcations found and their purpose
5’ cap : At the beginning of newly synthesized mRNA, consists of guanasine, 3 phosphates and a methyl group, important for translational machinery later
Poly-A tail: found on newest part or 3’ end of new mRNA , protects fron degrdation
What is splicing? When does it occur?
separating coding stretches from transcripts from non coding, separating exons and introns of Eukaryotic transcript.
Coding regions (exons - “expressed”) are kept
Non coding regions (introns) are discarded
Occurs when mRNA is still being transcribed after capping
What is the difference between primary RNA transcript and spliced (mature) transcript
Primary RNA transcript: includes exons and introns
Spliced transcript: includes only the exons
How are introns spliced and by what? What happens to introns after?
A branch point cuts the sugar phosphate backbone of the intron area. Done with spliceosomes (a RNA protein complex)
These cut ends forms covalent bonds with ribose sugar group to form a lariat strucutre
Which is eventually degraded in the nucleus
What type of mRNA can be exported from nucleus? What are those conditions?
mature mRNA
- cap and poly A tail are marked by proteins
- group of proteins binds properly to spliced mRNAs
then mRNA can transport out of nuclear pore
How is an amino acid specified?
Takes 3 bases from RNA to form a code (amino acid)
Many codons can specify for one amino acid, with the exception of methionine (Met) and tryptophan (Trp)
How is the genetic code almost universal? What are some exceptions to this?
- same codons assigned to same amino acids
- same stop and start signals
Exceptions in mitochondria from animal cells:
- stop codon is a regular amino acid on mitochondria
What does the loss or gain of bases in genetic code/reading frame can result in?
frame shift mutation
How does an mRNA codon specify an amino acid?
with the help of aminoacyl tRNA .
Each amino acid has its own aminoacyl tRNA synthase
What do tRNA’s look like?
- Attached amino acid at the 3’ end
- anticodon at one side to pair with mRNA codon
What’s the wobble hypothesis?
The anticodon of tRNAs can still bind sucessfully to codon whose third base can vary
Describe the process of loading a tRNA, what is the purpose of this? What molecules are involved?
- purpose: to be able to put together the amino acid and its corresponding anticodons together
- This is done with the help of aminoacyl tRNA synthetase
- active site of synthetase binds ATP and amino acid
- AMP and amino acid are activated and bonded by the hydrolysis of ATP
- the tRNA specific to the amino acid comes to synthetase where the activated amino acid can be transferred to it.
This creates the finished aminoacyl
Role of small and large subunit of ribosomes in translation?
Small subunit; matches tRNAs to codons
Large subunit; catalyzes formation of peptide bonds
What are polyribosomes ? where does it occur? Why does it occur?
Refers to the translation of multiple mRNA simultaneously in both bacteria and eukaryotes. Because it allows the formation of more proteins from a single message
Where does simulataneous transcription and translation occur? Why?
in prokaryotes, because there are no nucleus
What are post-translational modification of eukaryotes? what are some examples? Why?
Addition of functional groups or small molecules onto protein structure after translation…
ex.
glycosylation
addition of lipid
phosphorylation
ubiquitnation
methyl/hydroxyl, acetyl lation
proteolysis (cleavage of peptde bonds)
For protein diversity
How does mRNA codon specify an amino acid
an adapter molecule, aminoacyl tRNA, consists of tRNA + amino acid
- help amino acids interact with corresponding codon on mRNA
- amino acid is attached at the top/3’ end of tRNA
- anticodon attached at the bottom that contains ribonucleotides that base pair with mRNA codon
Wobble Hypothesis
The anticodon of tRNAs can still bind successfully to a codon whose third position requires a nonstandard base paring
(tRNAs need accurate base-pairing at only the first two bases of a codon)
Describe the function of the large subunit of ribosomes
catalyzes formation of peptide bonds
What does tRNA must be loaded with
- each synthetase must recognize its amino acid plus all anticodons that recognize that amino acid
- hydrolysis of ATP to AMP will activate the amino acid to be transferred to tRNA
Describe the function of the small subunit of ribosomes
matches tRNAs to codons
When does translation begin
when the anticodon of a charged tRNA bonds to a codon in mRNA
When does translation end
When that amino acid forms a peptide bond with growing chain
Describe the E site, P site, and A site of ribosome
E site: holds tRNA that will exist
P site: holds tRNA with growing polypeptide attached
A site: holds AMINOACYL tRNA
once translation is ongoing, two of the three binding sites within ribosome are occupied by a tRNA at any given time
Describe the initiation of translation in eukaryotes
begins with codon AUG on mRNA that will be detected by small ribosomoal subunit containing tRNA MET (initiator tRNA) thats also binded to translation initiation factor
Then the large ribosomal subunit binds to small subunit
This allows for charged tRNA to bind to the A site
What initiates translation in eukaryotes
- aways begins with codon
Describe the termination of translation in eukaryotes
- when there is the presence of a stop codon in the mRNA (which is not recognized by a tRNA - do not specify an AA)
- A release factor will bind to this stop codon in the A site causing addition of water
- this releases everything
ribozyme
RNA molecule wth a well defined tertiary structure that enables it to catalyze a chemical rxn
How can bacteria and eukaryotes translate a protein faster
if more than one ribosome hops on the mRNA to translate many mRNA simultaneously
- called polyribosomes or polysomes
Can there be simultaneous transcription and translation in prokaryotes
before transcription is completed , translation can already be happening
When do proteins fold?
- begins during translation (before termination and disassembly of ribosomes)
- occurs spontaneously (no NRG required) with the help of chaperone proteins
Post translation modification of protein structure
- generally involves the addition of functional groups or small molecules
- glycosylation
- addition of lipid
- phosphorylation
- ubiquination
- methylation, hydroxylation, acetylation
- proteolysis (cleavage of peptide bonds)
