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Molecular Genetics > Translation/Epigentics > Flashcards

Translation/Epigentics Flashcards

1
Q

Translation

A

synthesis of a protein on an RNA template

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2
Q

mRNA

A

has the codons for the amino acids of the protein

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2
Q

Aminoacyl-tRNAs

A
  • has the anti-codons for the amino acids of the protein
  • and carries the specific amino acid
  • tRNA with attached amino acid
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3
Q

Ribosome

A
  • the ribonucleoprotein machine that puts the amino acids together
  • has a large and small subunit
    made of both protein and rRNA
  • ribonucleoprotein has more RNA than protein
  • ribosomes contain several active centers
  • rRNA and protein both have catalytic roles
  • proteins cannot function alone, only in the context of the ribosome
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4
Q

tRNA

A
  • all have -CAA-3’ end (where amino acid attaches)
  • anti-codon at the other end
  • at least on tRNA for every amino acid used by the cell
  • “L” shape
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5
Q

active centers

A

places where reactions or bindings occur

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6
Q

tRNA binding in the ribosome

A
  • the aminoacyl end of the tRNA is in the large subunit
  • the anticodon end is bound by the small subunit
  • the mRNA is bound by the small subunit
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7
Q

A site

A
  • aminoacyl-tRNA binding site
  • new tRNA with the next amino acid binds
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8
Q

P site

A
  • peptidyl-tRNA binding site
  • tRNA bound to the growing peptide chain
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9
Q

E site

A
  • deacylated tRNA transiently bound
  • deacylated tRNA is leaving the ribosome
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10
Q

Aminoacyl-tRNA binding sites

A
  • tRNA is mostly in contact with the rRNA
  • mRNA must “kink” to allow simultaneous anticodon binding at the A site and P site
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11
Q

What are the 3 steps for translation?

A
  1. Initiation
  2. Elongation
  3. Termination
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12
Q

Initiation

A
  • ribosome small subunit binds to the mRNA
  • large subunit binds to the small subunit
  • the first aminoacyl-tRNA binds to the P site
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13
Q

Elongation

A
  • Aminoacyl-tRNA for the next codon enters the A site
  • initial amino acid or the growing polypeptide chain in the P site
  • Polypeptide chain is transferred to the aminoacyl-tRNA in the A site (peptide bond is formed)
  • translocation occurs next
  • movement of ribosome along the mRNA
  • transfers the deacylated tRNA to the E site
  • moves the now peptidyl-tRNA to the P site (A site now empty)
  • the next aminoacyl-tRNA moves into the A site
  • cycle starts again, is the most rapid part of translation
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14
Q

peptide bond

A

the carboxyl group of one amino acid is bound to the amino group of another forming a peptide bond

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15
Q

Termination

A
  • the final deacylated tRNA is released
  • the new protein chain is released
  • the ribosome subunits dissociate from the mRNA
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16
Q

Bacterial Initiation requires initiation factors (IF)

A
  • IF3
  • IF2
  • IF1
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16
Q

Translation Initiation in Bacteria

A
  • initiation occurs at a special mRNA sequence
  • ribosome-binding site
  • is upstream of the coding region
  • complementary to a section of the rRNA of the 30S small ribosome subunit
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17
Q

IF2

A
  • brings the initiator aminoacyl-tRNA to the P site
  • has GTPase activity (possibly to help the joined subunits to form the functional 70S ribosome)
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17
Q

IF3

A
  • stabilizes free small ribosome (30S) subunits (large and small ribosome subunits must be separate)
  • inhibits binding of the large ribosome (50S) subunit
  • checks the accuracy of recognition of the first aminoacyl-tRNA
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18
Q

IF1

A

binds to the small subunit ribosome to complete initiation

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19
Q

How does the cell know this AUG is the actual start site?

A
  • AUG codes for a special initiator tRNA
  • 2 types of tRNAs for Met in bacteria (usual Met and N-Formyl-methionyl-tRNAf)
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20
Q

N-Formyl-methionyl-tRNAf

A
  • blocked amino group, cannot be used in peptide chain elongation
  • IF2 is responsible for bringing the first aminoacyl-tRNA to the P site, that is fMet-tRNAf
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21
Q

Eukaryotic Initiator Met-tRNAi

A
  • initiator tRNA Met is NOT formylated
  • specific for initiation has:
  • different folded structure
    is phosphorylated on base 64
  • cannot be used for elongation
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22
Q

Eukaryotic Initiation Factors

A

elF3, elF2, elF1A, elF1, Met-tRNAi, and 40S ribosome

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23
Q

elF3

A
  • binds to the 40S small ribosome subunit
  • prevents the 60S large subunit from binding
24
Q

Cap-Binding Complex

A
  • many elFs bind to the 5’ cap end of the mRNA
  • the complex binds to the 3’ end of the mRNA
  • then the complex binds to the pre-initiation complex
  • this huge complex “scans” the mRNA from the 5’ cap to find the AUG initiation site
24
Q

elF2

A
  • binds the Met-tRNAi
  • then, binds to the 40S small ribosome subunit
25
Q

elF1 and elF1A

A

both then bind to the 40S small ribosome subunit

26
Q

Elongation: Aminoacyl-tRNA loading

A
  • aminoacyl-tRNAs are brought to the ribosome by EF-Tu
27
Q

EF-Tu

A
  • a monomeric G-protein
  • a molecular switch protein
  • when GTP is bound = active
  • reactivate by replacing GDP with GTP
28
Q

EF-Tu cycle

A
  • EF-Tu-GTP binds an aminoacyl-tRNA
  • aminoacyl-tRNA-EF-Tu-GTP binds to the A site of the ribosome
  • aminoacyl-tRNA anticodon end binds to the A site
  • the anticodon pairs with codon
  • binding of the anticodon to the codon causes a conformational shift in the ribosome
    tRNA binding is stabilized, then EF-Tu hydrolyzes GTP to GDP
  • EF-Tu no longer binds to tRNA and EF-Tu is released
  • EF-Tu is recycled by switching GDP to GTP
29
Q

Peptidyl transferase

A

of the large subunit does the transfer from tRNA in the P site to the new tRNA in the A site and synthesizes the peptide bond

30
Q

Translocation of the ribosome

A
  • the movement of the ribosome 3 nucleotides along the mRNA
  • requires another monomeric G protein EF-G
31
Q

EF-G

A
  • after the peptide is shifted to the new tRNA in the A site,
  • EF-G-GTP binds to the ribosome
  • EF-G hydrolyzes the GTP to GDP
  • causes a conformational change in the EF-G to force the ribosome to change shape
  • EF-G-GDP is released
  • this conformational change cause the ribosome to move 3 nucleotides over and moves the peptidyl-tRNA from the A site to the P site
  • the deacylated tRNA is moved to the E site and released into the cytoplasm
  • a site is now open for a new aminoacyl-tRNA
32
Q

Translation termination

A
  • use 3 termination codons (UAG, UAA, UGA)
  • there are no tRNAs that can pair with these codons
33
Q

missense mutations

A

point mutations that changed an amino acid in a polypeptide

34
Q

nonsense mutations

A
  • point mutations that led to premature termination
  • generated a termination codon
35
Q

RF1 or RF2

A
  • recognize and bind to the termination codons
  • activate the ribosome to hydrolyze the peptidyl-tRNA
  • to release the polypeptide from the tRNA
36
Q

Ribosome recycling factor (RRF)

A
  • causes release of the deacylated tRNA and mRNA
  • Then EF-G causes RRF release and thus ribosome dissociation
36
Q

RF3

A

cause release of RF1 or RF2

37
Q

Eukaryotic transcription vs. translation

A
  • transcriptions occurs exclusively in the nucleus
  • mRNA is then transported to the cytoplasm
  • Translation occurs in the cytoplasm
38
Q

Bacterial transcription vs translation

A
  • both occur in the same compartment of Bacteria
  • as soon as the mRNA appears during transcription, ribosomes begin to attach and begin translation
  • multiple ribosomes move along the mRNA as it is being produced
  • but bacterial mRNAs exist for only minutes because nucleases begin to degrade them
39
Q

frameshift errors

A
  • skipping a base or reading the codon twice
  • very rare
  • ribosome error
40
Q

Incorrect aminoacyl-tRNA (mis)pairing with the codon

A
  • wrong amino acid is incorporated
  • more common
41
Q

Epigenetics

A
  • changes that influence the phenotype without altering the genotype
  • changes in the properties of a cell that are inherited - but that do not represent a change in genetic information
  • two individuals, or two cells, with the same DNA sequence at a locus may have different phenotypes
42
Q

Inherited

A
  • inherited by offspring of an organism (meiosis)
  • inherited by daughter cells after cell replication (mitosis)
43
Q

epigenome

A

consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism’s offspring

44
Q

How does epigenetics work?

A
  • epigenome
  • epigenetic tags act as a kind of cellular memory
  • a cells epigenetic profile - a collection of tags that tell genes whether to be on or off - is the sum of the signals it has receive during its lifetime
45
Q

3 thins that can sustain epigenetic effects

A
  1. covalent modification of DNA (methylation of DNA
  2. A proteinaceous structure that assembles on DNA (proteins associating with chromatin)
  3. A protein aggregate that controls the conformation for new subunits as they are synthesized (prions)
46
Q

DNA methylation

A
  • principally occurs at CpG islands
  • fully methylated: methylated on the Cs in both directions
  • hemi methylated: only on one C in the DNA duplex is methylated
  • methylation suppresses gene expression
  • in a cell with two alleles on a homologous chromosomes -> one is methylated and the other is not
  • after replication -> one set is hemi methylated and one is not methylated
  • the hemi methylated gets methylated and results in inactive gene
47
Q

Proteins that associated with chromatin

A
  • heterochromatin is created by proteins that associate with histones
  • after DNA replication and cell division -> heterochromatin has half the proteins on the histones
  • so new proteins must be recruited to bind to histones
48
Q

Position-effect variegation (PEV)

A
  • genes can be active or silenced depending on how close they are to the heterochromatin boundary
  • seen in Drosophila
  • some cells may have an active gene, while in others it is inactive
  • heterochromatin inactivation can spread into active genes
  • After a point, this may be stably inherited by the daughter cells
49
Q

Formation of Heterochromatin

A
  1. Nucleation: occurs at a specific DNA sequence or region
  2. Propagation: the inactivation structure moves along the chromatin fiber until it is stopped
50
Q

How far heterochromatin propagates

A
  • may depend upon the quantity of heterochromatin proteins available
  • more proteins available = further spreading
  • insulators: DNA sequences that prevent an activating or inactivating effect from passing across
  • insulators are boundary elements
  • they protect active promoters from inactivation
51
Q

How chromatin is inactivated

A
  1. condensation of chromatin
    - makes the gene inaccessible to the transcription mechanism
    - tightly wound and compacted is unavailable
  2. Addition of proteins that directly block access to regulatory sites
  3. Proteins that directly inhibit transcription
52
Q

Su(var) genes

A
  • act to suppress variegation
  • genes for the formation of heterochromatin
  • histone deacetylases
  • heterochromatin proteins
53
Q

E(var) gene

A
  • act to enhance variegation
  • genes for the activating gene expression
    SWI/SNF chromatin remodeling complex
54
Q

Su(var) proteins

A
  • HP1 (heterochromatin protein 1)
  • has a chromodomain on the N-terminus
  • has a chromo shadow domain on the C-terminus (interacts with many other proteins)
55
Q

Model for heterochromatin formation

A
  • histone deacetylase (HDAC) removes acetylation of histone H3
  • histone methyltransferase methylates H3
  • creates a binding site for the chromodomain on HP1
  • the binding of HP1 can be a nucleation event
  • this can lead to a propagation event, or spreading of the heterochromatin
56
Q

Extension of heterochromatin

A
  • methylation and then binding of HP1
  • allows for more HP1 to bind
  • extending heterochromatin
  • the propagation event
57
Q

Heterochromatin then

A
  • blocks the binding of chromatin remodelers
  • obscures DNA binding sites from transcription factors
  • to inhibit gene activation and transcription
58
Q

Heterochromatin at telomers

A
  • due to SIR genes (silent information regulators)
  • binding of SIR proteins can silence any gene
  • but specifically allows silencing at telomers
  • interstitial telomeric sequences (ITSs): consist of random repeats of the canonical telomeric repeat, localized at interstitial sites -> between the centromeres and the telomeres

Molecular Genetics (5 decks)

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