L5. Gene expression & protein synthesis I Flashcards
explain the cellular control of gene expression
- if cell A in an organism needs protein A, it will make a lot of transcripts for protein A, upregulating it, but not a lot of protein B, deregulating it
- if cell B in the same organism needs protein B, it will up regulate protein B while deregulating protein A
cellular control of gene expression - stem cells
- cells that can differentiate into different kinds of cell
- can do this through up regulation and deregulation of certain proteins
define transcription
an ongoing process which occurs in many places at the same time (even for the same gene)
how is RNA different from DNA
- single strand
- U instead of T
- ribose sugar
how is DNA different from RNA
- double strand
- T instead of U
- deoxyribose sugar
DNA - what is the coding strand
- oriented in a 5’ to 3’ fashion
- looks like the finished mRNA
DNA - what is the template strand
- oriented in a 3’ to 5’ fashion
- strand that is used to make the mRNA
explain the intramolecular base-pairing of RNA
- RNA is not linear, it may go conventional or nonconventional base pairings
- it can form 3D structures to allow things to bind to it and interact with it
- these structures all have different functions
intermolecular base-pairing of RNA - conventional vs nonconventional base pairing
- conventional base pairing: A-U, G-C
- nonconventional: G-U, C-A
explain how RNA polymerase carries out transcription
- since DNA is not hydrogen bounded, it can be easily displaced and allow the RNA pol to transcript the code
- RNA pol uses mRNA molecules from 5’ to 3’
- to begin translation, it jumps onto the promoter region and recognizes the start codon
how is RNA pol different from DNA pol
- uses ribonucleotides
- doesn’t need a primer for transcription
- does not have the capacity for proofreading
- more mistakes
how is DNA pol different than RNA pol
- uses dNTPs
- needs primers for transcription
- does have the capacity for proofreading
- less mistakes
RNA pol vs DNA pol - why did RNA pol evolve to be mistake prone and DNA pol did not
- if there is a mutation in an mRNA, the mutation will be passed onto a small number of proteins
- if there is a mutation in DNA, then the mistake impacts the whole cell and thus all of the protein
- so its less dangerous if there is a mutation in RNA
explain the types of RNA molecules
- messenger RNAs (mRNAs)
- ribosomal RNAs (rRNAs)
- microRNAs (miRNAs)
- transfer RNAs (tRNAs)
- other noncoding RNAs
types of RNA - mRNA function
code for proteins
types of RNA - rRNA function
- form the core of the ribosome’s structure
- catalyze protein synthesis
types of RNA - miRNA function
regulate gene expression
types of RNA - tRNA function
serve as adaptors between mRNA and amino acids during protein synthesis
types of RNA - other noncoding RNA function
- used in RNA splicing
- gene regulation
- telomere maintenance
- many other processes
explain transcription in bacteria
bc there is no nucleus, transcription of mRNA and translation into a protein can happen at the same time
bacterial transcription - sigma factor
- recognizes promoter region and tells RNA pol to make mRNA
- it zips along the DNA (without unwinding it) with RNA pol until is encounters a promoter region
- then mRNA is made
bacterial transcription - promoter
- tells RNA pol to make mRNA
- has certain repeat sequences
- it is upstream of the starting point for RNA synthesis
- it will not be in the mRNA when transcription is done
how can genes be transcribed in different directions
- polymerases can use either on of the DNA strands as a template
- the promoter is always near the 3’ end and transcription occurs in the opposite direction towards 5’
how is prokaryotic RNA pols different than eukaryotic pols
- 1 RNA pol
- not a lot of regulatory elements
- genes are closer together
- RNA pol and sigma factor initiates transcription
how is eukaryotic RNA pols different than prokaryotic RNA pols
- 3 RNA pols
- RNA pols need accessory proteins: general transcription factors
- transcription initiation is more complicated
- many regulatory sequences, more complex regulation, genes further apart
- transcription has to take into account DNA packaging (nucleosomes)
eukaryotic transcription - RNA pol I
transcribes most rRNA genes
eukaryotic transcription - RNA pol II
transcribes:
- all protein-coding genes
- miRNA genes
- plus genes for noncoding RNAs
eukaryotic transcription - RNA pol III
transcribes: tRNA genes, 5S rRNA gene, and genes for many other small RNAs
explain eukaryotic transcription
- first, a transcription factor needs to find the TATA box (the promoter region)
- another transcription factor will recruit RNA pol to the box
- another transcription factor hydrolyzes ATP for energy
- another transcription factor uses the energy to phosphorylate the pol tail to allow enzymes to bind on it
eukaryotic transcription - what enzymes bind on the pol tail
- enzymes for capping, splicing, and polyadenylation
- the polyadenylation signal, signals the end of transcription
eukaryotic transcription - explain RNA processing
- RNA as to be processed before leaving the nucleus
- to leave the nucleus, it has to have a 5’ cap and a poly-A tail
eukaryotic transcription: mRNA processing - mRNA capping
- this refers to the modification of the mRNA 5’ end
- the capping results in an addition of a guanine with a methyl group
- happens when ~25 nucleotides have been transcribed
eukaryotic transcription: mRNA processing - polyadenylation
- first, the 3’ end is trimmed by an enzyme
- next, a second enzyme adds a series of repeated adenines
- happens after the noncoding sequence
- this attracts relevant proteins to bind onto the RNA pol II tail
eukaryotic genes - introns
- noncoding sequence
- cut by splicing factors before final mRNA is released
eukaryotic genes - exons
- represented in the open reading frame as coding sequences
- splicing factors glue them together after introns are taken out
eukaryotic genes - why is it advantageous to have more introns
- alternative splicing
- Can splice these in difference combinations and get different functions
- different versions of the same protein, made from the same gene, but with different functions
explain the splicing process
the spliceosome complex facilitates removal of intron and splicing of exons
how is mature mRNA reconigzed
- by RNA-binding proteins
- they recognize the 5’ cap, poly-A tail, and exon junctions and the mRNA will be exported out of the nucleus
splicing process - what is it regulated by
- snRNPs (small nuclear ribonucleic proteins)
- they interact with the spliceosome complex and recognizes exon-intron boundaries and removing introns
mature mRNA - what happens in the cytosol before translation
protein exchange in which 5’ cap binding protein is swapped for translation initiation factors
