gene expression Flashcards
what is the structure of RNA nucleotides
made up of a pentose sugar ribose, a phosphate group and a heterocyclic base that contains nitrogen and carbon (adenine, guanine, cytosine and uracil)
how do phosphodiester bonds form in RNA
between the alpha phosphate (first joined) and the 3’ end
why are RNA nucleotides less stable than DNA nucleotides
they have 2 hydroxyl groups so are more susceptible to hydrolysis as water interacts with the hydroxyl group
what is a wobble base pair in RNA
non-canonical base pairing between guanine and uracil
they affect the reading of the genetic code in translation
what is the structure of DNA-dependent RNA polymerases (RNAPs) and where does DNA bind
consists of 5 subunits: 2 alpha subunits, a larger beta and beta prime subunit and an omega subunit
DNA binds to the cleft between beta and beta primer subunits
what is the process of RNA transcription
- DNA is pulled apart to form a transcription bubble and the RNA sequence pairs to the DNA template strand
- RNAPs move along the coding strand to the promoter sequence and transcribe it into RNA
- nucleotide triphosphates (NTPs) are selected by base pairing and are added to the 3’ end of RNA
- proteins destabilise in the heteroduplex of RNAPs that causes RNA polymerase to be released from the terminator region of DNA to stop transcription
what are general transcription factors (gTF)
they assemble RNAP into gene promoters and bind RNA to transcription regions
what is the preinitiation complex (PIC)
a RNA polymerase bound to a promoter region
what are the 3 main types of RNA in a cell and their compositions
messenger RNA: 5%, unstable so degrade over time
ribosomal RNA: 75%, fewer in number than tRNA but larger
transfer RNA: 10%, most abundant in number
what is the first step (capping) in RNA processing
a guanosine nucleotide is added to the 5’ end of RNA making it resistant to hydrolysis
the cap is methylated for protection
what is the second step (splicing and cleaving) in RNA processing
- splice site sequences recognise introns and exons
- active spliceosomes are assembled when an intron is recognised by joining 5 snRNPs (small nuclear RNPs)
- an ester linkage is broken releasing the 5’ intron forming a lariat structure
- the exons are joined by an ester linkage and the intron lariat is released
what is the third step (polyadenylation) in RNA processing
adenylate residues are added to the 3’ end of mRNA preventing the ends from being degraded by nucleases
uses poly(A) polymerase
what is the main difference between eukaryotic and prokaryotic mRNA
eukaryotic mRNA can only be translated into one polypeptide (monocistronic)
prokaryotic mRNA can be translated into multiple different polypeptides (polycistronic)
what do tRNA molecules do
act as adaptor molecules
they bind to a ribosome which binds to mRNA and bring a specific amino acid for protein synthesis
they read the protein sequence in a 5’-3’ or N to C direction
what is the anticodon of a tRNA molecule
a sequence within tRNA that binds by complementary base pairing to the mRNA codon
how are tRNA molecules aminoacylated
when they are chemically joined to an amino acid
a peptide bond forms between the aminoacyl and peptidyl groups between adjacent tRNAs
why is the genetic code described as nonpunctuated
all nucleotides have genetic meaning and there are no spaces between the codons
codons read once
the sequence has 3 possible reading frames
why is the genetic code described as degenerate
there are more codon sequences than amino acids so some amino acids are coded for by more than one codon
which 2 amino acids are only coded for by one codon sequence
trp and met
why is the genetic code described as universal
the same codon codes for the same amino acid in all organisms
what are sense codons and how many are there
codons that code for a specific amino acid in a sequence
there are 61
what are non-sense codons and how many are there
they are either stop codons that mark the end of translation or start codons that begin translation
there are 3 stop codons: UAA, UAG, UGA
there is one stop codon: AUG
what are synonymous codons
codons that code for the same amino acid
they usually have the same fist and second nucleotides but a different third one
this shows that the 3rd nucleotide has the least effect on the genetic code
how are synonymous codons distinguished between
they can be recognised by different isoacceptor tRNAs which are tRNA molecules that are charged with the same amino acid but have different anticodons
they can also be recognised by the same tRNA with wobble base pairing
what is the secondary structure of a tRNA molecule
cloverleaf structure, the 5’ and 3’ ends are joined together forming a stem loop and the amino acid is attached to the 3’ hydroxyl group of the terminal adenosine nucleotide
all tRNA have a CCA nucleotide at the end of their sequence
what is the tertiary structure of a tRNA molecule
different tRNA molecules have different charges but all need a similar structure to bind to ribosomes
this is a 3D L shape
the two functional groups (amino acid and anticodon) are separated as they interact with different sites on the ribosome
what is coaxial stacking in tRNA molecules
the short tRNA helices stacking on top of each other to form the tertiary structure
what is the structure of ribosomes
they are large ribonucleoproteins (RNPs)
they have 2 subunits: a small subunits (SSU) and a large subunit (LSU)
they are highly conserved molecules (all have the same structure)
what is the interface region on a ribosome and what happens here
the point where the SSU and LSU meet
where protein synthesis occurs
codon-anticodon binding happens at the small subunit
peptide bond formation happens at the large subunit
what is the decoding centre on a ribosome
an area on the small subunit where mRNA is read and the amino acid is joined
what are the 3 binding sites on tRNA and what happens at each one
A: where the charged tRNA initially binds
P: where the tRNA moves to for peptide bond formation
E: the exit site where the tRNA is released from the ribosome
what is the peptidyl transferase centre on a ribosome
an area on the large subunit that contains lots of RNA and catalysed peptide bond formation and peptide released
this is called an RNA-catalysed reaction
what are methionyl-tRNA’s and what are the 2 forms
tRNA molecules that are charged with the amino acid methionine
initiated: directed to the P site
elongated: directed to the A site
what happens during translation initiation
- the ribosome is directed to the AUG start codon on mRNA
- the initiated tRNA interacts with EF2 and forms a preinitiation complex with the small subunit by interacting with the cap-binding complex (CBC)
- the small subunit scans along mRNA until it finds the start codon using energy from helicase activity of CBC
what is the kozak sequence in mRNA
a sequence of mRNA that contains the start codon
how are ribosomes initiated in bacterial mRNA
bacterial mRNA is polycistronic meaning it has multiple open reading frames so the ribosome is targeted to multiple start codons by interacting with the shine-delgado sequence
what happens during the translation elongation cycle
- the aminoacylated tRNA binds to the A site, there is already a tRNA in the P site and a peptide bond forms between the two amino acids
- the ribosome moves along mRNA causing the now uncharged tRNA to move from the P site to the E site and be released
- the charged amino acid moves to the P site and the cycle continues
how are GTPases used in the translation elongation cycle
hydrolyses GTP to GDP providing energy for protein synthesis
the charged tRNA is bound to the elongation factor 1 (EF1A) which brings it to the A site
translocation of the ribosome requires elongation factor 2 (EF2)
how is translation terminated
there are 2 protein termination factors
1. eukaryotic release factor 1 (ERF1) binds to the stop codon in the A site causing the peptide bond to be hydrolysed
2. eukaryotic release factor 3 (ERF3) hydrolyses GTP to GDP allowing ERF1 to be released so it can be reused
what are regulated and house-keeping genes
regulated genes are only expressed when the cell needs them
house-keeping genes are always expressed because they are always needed
what can happen if genes expression is not regulated
if gene expression is not regulated it can cause uncontrolled cell growth and cancer
what are trans-acting factors in gene expression
they are proteins that interact with specific DNA or RNA sequences called regulatory elements
they are products of genes that act on the expression of other genes
what are cis and trans mutations and where do they happen
cis: mutations within the same gene occurring in regulatory elements
trans: mutations in a different gene that occur in trans-acting factors
how is gene expression regulated in RNA processing
splicing can occur at different positions called splice sites
transcription factors recognise splice sites under different conditions to express different proteins of the same gene
how is gene expression regulated in translation initiation
translation of certain transcripts can be down-regulated to prevent gene expression
it can also be regulated by transcript-specific mechanisms such as availability of certain nutrients e.g. the protein ferritin is only made if iron levels are low
how does phosphorylation of EIF2 inhibit translation
during translation EIF2 hydrolyses GTP to GDP, it needs to be regenerated by EIF2B for translation to continue
when EIF2 is phosphorylated it binds tightly to EIF2B so it cant be regenerated and translation is inhibited
how do transcription factor affect gene expression
they can increase or decrease gene transcription and expression
activators positively control genes to express them
repressors negatively control genes to stop their expression
what are promoters
sequences of DNA that RNA polymerase binds to for transcription
they can be strong (high rate of transcription) or weak (low rate)
transcription factors bind to weak promoter regions
how is the activity of transcription factors affected
inducers stimulate transcription activators and inhibit repressors
corepressors stimulate transcription repressors and inhibit activators
what is the lac operon
a set of 3 genes that are involved in the digestion of lactose
the expression of lac operon is controlled by the transcription repressor gene lacl
how does the gene lacl affect expression of lac operon
when lactose isn’t present lacl binds to lac operon and blocks RNA polymerase activity so the gene isnt expressed
when lactose enters the body it inhibits lacl so lac operon is transcribed
what is catabolite activator protein (CAP)
a transcription activator that stimulates enzymes that hydrolyse non-glucose sugars
how does CAP affect expression of the lac operon
when glucose isn’t present CAP binds to lac promoter and stimulates transcription of lac operon
what are the 3 types of RNA polymerase and what do they do
RNA polymerase 1: transcribes ribosomal RNA genes
RNA polymerase 2: transcribes protein coding genes into mRNA
RNA polymerase 3: transcribes tRNA genes
