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molecular and cell biology > gene expression > Flashcards

gene expression Flashcards

(55 cards)

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1
Q

what is the structure of RNA nucleotides

A

made up of a pentose sugar ribose, a phosphate group and a heterocyclic base that contains nitrogen and carbon (adenine, guanine, cytosine and uracil)

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2
Q

how do phosphodiester bonds form in RNA

A

between the alpha phosphate (first joined) and the 3’ end

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3
Q

why are RNA nucleotides less stable than DNA nucleotides

A

they have 2 hydroxyl groups so are more susceptible to hydrolysis as water interacts with the hydroxyl group

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4
Q

what is a wobble base pair in RNA

A

non-canonical base pairing between guanine and uracil
they affect the reading of the genetic code in translation

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5
Q

what is the structure of DNA-dependent RNA polymerases (RNAPs) and where does DNA bind

A

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

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6
Q

what is the process of RNA transcription

A
  1. DNA is pulled apart to form a transcription bubble and the RNA sequence pairs to the DNA template strand
  2. RNAPs move along the coding strand to the promoter sequence and transcribe it into RNA
  3. nucleotide triphosphates (NTPs) are selected by base pairing and are added to the 3’ end of RNA
  4. proteins destabilise in the heteroduplex of RNAPs that causes RNA polymerase to be released from the terminator region of DNA to stop transcription
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7
Q

what are general transcription factors (gTF)

A

they assemble RNAP into gene promoters and bind RNA to transcription regions

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8
Q

what is the preinitiation complex (PIC)

A

a RNA polymerase bound to a promoter region

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9
Q

what are the 3 main types of RNA in a cell and their compositions

A

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

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10
Q

what is the first step (capping) in RNA processing

A

a guanosine nucleotide is added to the 5’ end of RNA making it resistant to hydrolysis
the cap is methylated for protection

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11
Q

what is the second step (splicing and cleaving) in RNA processing

A
  1. splice site sequences recognise introns and exons
  2. active spliceosomes are assembled when an intron is recognised by joining 5 snRNPs (small nuclear RNPs)
  3. an ester linkage is broken releasing the 5’ intron forming a lariat structure
  4. the exons are joined by an ester linkage and the intron lariat is released
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12
Q

what is the third step (polyadenylation) in RNA processing

A

adenylate residues are added to the 3’ end of mRNA preventing the ends from being degraded by nucleases
uses poly(A) polymerase

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13
Q

what is the main difference between eukaryotic and prokaryotic mRNA

A

eukaryotic mRNA can only be translated into one polypeptide (monocistronic)
prokaryotic mRNA can be translated into multiple different polypeptides (polycistronic)

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14
Q

what do tRNA molecules do

A

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

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15
Q

what is the anticodon of a tRNA molecule

A

a sequence within tRNA that binds by complementary base pairing to the mRNA codon

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16
Q

how are tRNA molecules aminoacylated

A

when they are chemically joined to an amino acid
a peptide bond forms between the aminoacyl and peptidyl groups between adjacent tRNAs

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17
Q

why is the genetic code described as nonpunctuated

A

all nucleotides have genetic meaning and there are no spaces between the codons
codons read once
the sequence has 3 possible reading frames

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18
Q

why is the genetic code described as degenerate

A

there are more codon sequences than amino acids so some amino acids are coded for by more than one codon

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19
Q

which 2 amino acids are only coded for by one codon sequence

A

trp and met

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20
Q

why is the genetic code described as universal

A

the same codon codes for the same amino acid in all organisms

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21
Q

what are sense codons and how many are there

A

codons that code for a specific amino acid in a sequence
there are 61

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22
Q

what are non-sense codons and how many are there

A

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

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23
Q

what are synonymous codons

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A

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

24
Q

how are synonymous codons distinguished between

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A

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

25
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
26
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
27
what is coaxial stacking in tRNA molecules
the short tRNA helices stacking on top of each other to form the tertiary structure
28
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)
29
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
30
what is the decoding centre on a ribosome
an area on the small subunit where mRNA is read and the amino acid is joined
31
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
32
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
33
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
34
what happens during translation initiation
1. the ribosome is directed to the AUG start codon on mRNA 2. the initiated tRNA interacts with EF2 and forms a preinitiation complex with the small subunit by interacting with the cap-binding complex (CBC) 3. the small subunit scans along mRNA until it finds the start codon using energy from helicase activity of CBC
35
what is the kozak sequence in mRNA
a sequence of mRNA that contains the start codon
36
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
37
what happens during the translation elongation cycle
1. 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 2. the ribosome moves along mRNA causing the now uncharged tRNA to move from the P site to the E site and be released 3. the charged amino acid moves to the P site and the cycle continues
38
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)
39
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
40
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
41
what can happen if genes expression is not regulated
if gene expression is not regulated it can cause uncontrolled cell growth and cancer
42
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
43
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
44
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
45
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
46
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
47
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
48
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
49
how is the activity of transcription factors affected
inducers stimulate transcription activators and inhibit repressors corepressors stimulate transcription repressors and inhibit activators
50
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
51
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
52
what is catabolite activator protein (CAP)
a transcription activator that stimulates enzymes that hydrolyse non-glucose sugars
53
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
54
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
55

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