Translation Flashcards
Problems with lacking telomerase
Prone to cancer Premature aging (more and more mutations in cells)
Telomerase disease
Dyskeratosis congenita- carry a mutant telomerase RNA gene
Die of progressive bone marrow failure- bone marrow produces immune system cells-patients will die from infection
Exonuclease activity
It recognizes error and fixes it on the spot
Cellular organisms need high fidelity replication
Germ cells need low mutation rates to maintain species
Somatic cells need low mutation rates to avoid uncontrolled proliferation/cancer
Ionizing radiation
X-rays
DNA to protein cross-links
Causes double-stranded breaks
Most common way of passing bad genes to offspring
Deamination of Methylated cytosines
You can lose an amine group and turns it into Thymine (C–>T). Most common form of mutation
A special DNA glycosylase recognizes and removes the T
Methylation silences gene expression.
Transcription coupled repair (TCR)
Recognizes bad base pairs as RNA is being synthesized. The enzymes stop transcription so that it doesn’t make a lot of bad proteins
RNA is not the hereditary information…why?
It cannot distinguish between deaminated Cytosine and natural Uracil
Thymine dimer repair
UV radiation can cause thymine dimers
Enzyme can break bond and is light dependent. Recognizes dimer and requires light to break bond
Photolyase
mRNA
Only coding RNA’s
snRNA
Small nuclear RNA
direct the splicing of pre-mRNA to form mRNA
siRNA
Small interfering RNA
regulate eukaryotic gene expression by degrading select mRNA
Used for knocking out RNA
miRNA
Micro RNA
regulate gene expression by blocking translation of selective mRNA
RNA pol 1, 2, 3
1, 2, 3= m, r, t
mRNA
rRNA
tRNA
TATA box/CAAT box
Common promoters
Elevated glucocorticoid or thyroxine…
The PEPCK gene will be activated and you will have lots of gluconeogenesis
TFIIH
Has helicase activity and kinase activity (phosphorylates the tail of polymerase to leave the complex)
Defects: leads to:
- Xeroderma pigmentosum: skin very sensitive, prone to melanomas and carcinomas (NER complex is defective and can’t fix UV induced thymine dimers)
- Cockayne syndrome:
- Trichothiodystrophy
Termination sequences
A-T rich
Followed by poly(U) tail
Hairpin loop formed which makes RNA polymerase fall off
Homeodomain proteins
Bind to DNA and help w/ turning off/on transcription
Zinc fingers
Rich in Cys and His
They form hooks on DNA and helps control transcription
Cancer and TF’s
Most cancers are caused by defects in TF’s (especially those that regulate growth)
FMR1
Methylation: silences gene. Messes up promoter and so transcription doesn’t work right and so you don’t get the FMR1 protein being made
Structure of puromycin and tyrosyl-tRNA
Instead of Tyrosyl-tRNA, your Puromycin gets incorporated into the chain. The system recognizes that it’s not the right AA and terminates translation and so you don’t get the proteins that are useful for the synthesis of bacteria
Polysomes
Clusters of ribosomes and bind to single mRNA molecule. Makes protein synthesis more efficient
Mitochondrial Protein synthesis
Peptidyl transferase (enzyme that forms peptide bond) is sensitive to the antibiotic chloramphenicool
Basically mitochondrial RNA resembles prokaryote system more
Missense Mutation
Change in AA in protein that may have an effect on protein function
Proteins are synthesized in what direction?
Amino to carboxyl direction by adding on AA’s to the carboxyl end
Silent mutation
Does not change the AA
Missense mutation
Mutations result in one AA being replaced by another (e.g. CGA to CCA causes arginine to be replaced by proline)
e.g. Sickle cell anemia (point mutation)
Nonsense mutation
Codon changes into a stop codon causing premature chain termination. Also called null mutation. Protein either degraded or formed as a truncated version.
Frameshift mutation
Occur when the number of bases added or deleted is not a multiple of three. The reading frame is shifted so that completely different sets of codons are read beyond the point where the mutation starts
tRNA structure
Cloverleaf
Important regions:
- Anticodon loop: set of 3 nucleotides that pair with codon on mRNA
- 3’ CCA terminal region: binds the AA that matches the corresponding codon
Aminoacyl-tRNA synthetase
Attaches the appropriate amino acid onto its tRNA.
Parts of eukaryotic ribosome
80S (40S and 60S subunits)
Parts of prokaryotic ribosome
70S (30S and 50S subunits)
What does eukaryotic mRNA have on it?
7-methylguanosine cap at 5’ end
poly(A) tail at 3’ end
Eukaryotic initiation: binding of mRNA to small ribosomal subunit
- Cap at 5’ end of mRNA binds eIFs
- Binds 40S ribosomal subunit containing tRNA met. 3. mRNA is scanned for AUG start codon within the Kozak consensus sequence
- Large subunit (60S) joins
1st AA: methionine
IF’s: eIFs (12 or more)
Initation
- Small subunit binds to initiator tRNA which is carrying methionine (1st AA of soon-to-be-made chain)
- This complex attaches to 5’ cap of mRNA and scans for AUG start codon
- IF’s help (eIF1, eIF2, eIF3, GTP)
- At start codon, large subunit joins and IF’s are released
Peptide bond between AA’s in A and P site in ribosome is catalyzed by what?
Peptidyl transferase
Elongation factors
Makes translation more efficient and accurate
Bacteria: EF-Tu and EF-G
Euk: EF1 and EF2
EF-Tu binds GTp and the aminoacyl tRNA. Escorts it to ribosome to make sure tRNA matches correctly
Interactions of EF-Tu, tRNA and ribosome introduce critical proof-reading
GTP hydrolysis brings about conformation changes in ribosomes that facilitates dissociation
What does streptomycin do?
Binds to 30S subunit to disrupt initiation of translation
What does Shiga toxin do?
Shiga toxin binds to the 60S subunit to disrupt elongation
What do Clindamycin and erythromycin do?
Bind to 50S subunit to disrupt translocation of the ribosome
What does Tetracycline do?
Binds to the 30S subunit to disrupt elongation
What does peptidyl transferase do?
Peptidyl transferase activity is housed in the large subunit
What do initiation factors do that are on the small subunit?
Facilitate the binding of the small subunit to the initiator tRNA and base pairing between the anticodon and codon
Prok: IF-1, IF-3
Euk: eIF1, eIF1A, eIF3, eIF5
What do initiation factors do that are on the initiator tRNA?
Hydrolysis of GTP to GDP +P provides energy for assembly of initiation complex
Prok: IF-2-GTP
Euk: eIF2-GTP
What else is needed for assembling the final 80S initiation complex?
Additional initiation factors such as the eIF4 complex and eIF5B-GTP are required for the assembly of the final 80S initiation complex
Structure of puromycin vs tyrosyl-tRNA
Puromycin resembles the aminoacylated 3’ end of tyrosyl-tRNA!!!
DNA polymerase 𝛿
Polymerase 𝛿: synthesizes okazaki fragments
Flap endonuclease 1 (FEN1)
Removes RNA primers (DNA Pol 1 in prokaryotes)
DNA polymerase α (in complex with primase)
Synthesizes RNA-DNA primer
DNA Damage by Chemical Agents
- Agents that require metabolic activation: benzopyrene (cigarette smoke, exhaust, charred meats)-inhibits tumor suppressor genes–>carcinogen, aflatoxin B1
Agents that act directly to modify DNA
Cross-linking agents: Nitrogen mustard, mitomycin C (cancer chemotherapeutic agents)
Alkylating Agents: dimethyl sulfate (DMS), methylmethane sulfonate (MMS)
Intercalating agents: ethidium bromide etc
