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Biochemistry > Translation > Flashcards

Translation Flashcards

1
Q

Problems with lacking telomerase

A 
Prone to cancer
Premature aging (more and more mutations in cells)
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2
Q

Telomerase disease

A

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

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3
Q

Exonuclease activity

A

It recognizes error and fixes it on the spot

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4
Q

Cellular organisms need high fidelity replication

A

Germ cells need low mutation rates to maintain species

Somatic cells need low mutation rates to avoid uncontrolled proliferation/cancer

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5
Q

Ionizing radiation

A

X-rays

DNA to protein cross-links

Causes double-stranded breaks

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6
Q

Most common way of passing bad genes to offspring

A

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.

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7
Q

Transcription coupled repair (TCR)

A

Recognizes bad base pairs as RNA is being synthesized. The enzymes stop transcription so that it doesn’t make a lot of bad proteins

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8
Q

RNA is not the hereditary information…why?

A

It cannot distinguish between deaminated Cytosine and natural Uracil

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9
Q

Thymine dimer repair

A

UV radiation can cause thymine dimers

Enzyme can break bond and is light dependent. Recognizes dimer and requires light to break bond

Photolyase

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10
Q

mRNA

A

Only coding RNA’s

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11
Q

snRNA

A

Small nuclear RNA

direct the splicing of pre-mRNA to form mRNA

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12
Q

siRNA

A

Small interfering RNA

regulate eukaryotic gene expression by degrading select mRNA

Used for knocking out RNA

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13
Q

miRNA

A

Micro RNA

regulate gene expression by blocking translation of selective mRNA

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14
Q

RNA pol 1, 2, 3

A

1, 2, 3= m, r, t

mRNA
rRNA
tRNA

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15
Q

TATA box/CAAT box

A

Common promoters

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16
Q

Elevated glucocorticoid or thyroxine…

A

The PEPCK gene will be activated and you will have lots of gluconeogenesis

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17
Q

TFIIH

A

Has helicase activity and kinase activity (phosphorylates the tail of polymerase to leave the complex)

Defects: leads to:

  1. Xeroderma pigmentosum: skin very sensitive, prone to melanomas and carcinomas (NER complex is defective and can’t fix UV induced thymine dimers)
  2. Cockayne syndrome:
  3. Trichothiodystrophy
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18
Q

Termination sequences

A

A-T rich

Followed by poly(U) tail

Hairpin loop formed which makes RNA polymerase fall off

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19
Q

Homeodomain proteins

A

Bind to DNA and help w/ turning off/on transcription

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20
Q

Zinc fingers

A

Rich in Cys and His

They form hooks on DNA and helps control transcription

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21
Q

Cancer and TF’s

A

Most cancers are caused by defects in TF’s (especially those that regulate growth)

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22
Q

FMR1

A

Methylation: silences gene. Messes up promoter and so transcription doesn’t work right and so you don’t get the FMR1 protein being made

23
Q

Structure of puromycin and tyrosyl-tRNA

A

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

24
Q

Polysomes

A

Clusters of ribosomes and bind to single mRNA molecule. Makes protein synthesis more efficient

25
Q

Mitochondrial Protein synthesis

A

Peptidyl transferase (enzyme that forms peptide bond) is sensitive to the antibiotic chloramphenicool

Basically mitochondrial RNA resembles prokaryote system more

26
Q

Missense Mutation

A

Change in AA in protein that may have an effect on protein function

27
Q

Proteins are synthesized in what direction?

A

Amino to carboxyl direction by adding on AA’s to the carboxyl end

28
Q

Silent mutation

A

Does not change the AA

29
Q

Missense mutation

A

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)

30
Q

Nonsense mutation

A

Codon changes into a stop codon causing premature chain termination. Also called null mutation. Protein either degraded or formed as a truncated version.

31
Q

Frameshift mutation

A

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

32
Q

tRNA structure

A

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
33
Q

Aminoacyl-tRNA synthetase

A

Attaches the appropriate amino acid onto its tRNA.

34
Q

Parts of eukaryotic ribosome

A

80S (40S and 60S subunits)

35
Q

Parts of prokaryotic ribosome

A

70S (30S and 50S subunits)

36
Q

What does eukaryotic mRNA have on it?

A

7-methylguanosine cap at 5’ end

poly(A) tail at 3’ end

37
Q

Eukaryotic initiation: binding of mRNA to small ribosomal subunit

A
  1. Cap at 5’ end of mRNA binds eIFs
  2. Binds 40S ribosomal subunit containing tRNA met. 3. mRNA is scanned for AUG start codon within the Kozak consensus sequence
  3. Large subunit (60S) joins

1st AA: methionine
IF’s: eIFs (12 or more)

38
Q

Initation

A
  1. Small subunit binds to initiator tRNA which is carrying methionine (1st AA of soon-to-be-made chain)
  2. This complex attaches to 5’ cap of mRNA and scans for AUG start codon
  3. IF’s help (eIF1, eIF2, eIF3, GTP)
  4. At start codon, large subunit joins and IF’s are released
39
Q

Peptide bond between AA’s in A and P site in ribosome is catalyzed by what?

A

Peptidyl transferase

40
Q

Elongation factors

A

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

41
Q

What does streptomycin do?

A

Binds to 30S subunit to disrupt initiation of translation

42
Q

What does Shiga toxin do?

A

Shiga toxin binds to the 60S subunit to disrupt elongation

43
Q

What do Clindamycin and erythromycin do?

A

Bind to 50S subunit to disrupt translocation of the ribosome

44
Q

What does Tetracycline do?

A

Binds to the 30S subunit to disrupt elongation

45
Q

What does peptidyl transferase do?

A

Peptidyl transferase activity is housed in the large subunit

46
Q

What do initiation factors do that are on the small subunit?

A

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

47
Q

What do initiation factors do that are on the initiator tRNA?

A

Hydrolysis of GTP to GDP +P provides energy for assembly of initiation complex

Prok: IF-2-GTP
Euk: eIF2-GTP

48
Q

What else is needed for assembling the final 80S initiation complex?

A

Additional initiation factors such as the eIF4 complex and eIF5B-GTP are required for the assembly of the final 80S initiation complex

49
Q

Structure of puromycin vs tyrosyl-tRNA

A

Puromycin resembles the aminoacylated 3’ end of tyrosyl-tRNA!!!

50
Q

DNA polymerase 𝛿

A

Polymerase 𝛿: synthesizes okazaki fragments

51
Q

Flap endonuclease 1 (FEN1)

A

Removes RNA primers (DNA Pol 1 in prokaryotes)

52
Q

DNA polymerase α (in complex with primase)

A

Synthesizes RNA-DNA primer

53
Q

DNA Damage by Chemical Agents

A
  1. Agents that require metabolic activation: benzopyrene (cigarette smoke, exhaust, charred meats)-inhibits tumor suppressor genes–>carcinogen, aflatoxin B1
54
Q

Agents that act directly to modify DNA

A

Cross-linking agents: Nitrogen mustard, mitomycin C (cancer chemotherapeutic agents)

Alkylating Agents: dimethyl sulfate (DMS), methylmethane sulfonate (MMS)

Intercalating agents: ethidium bromide etc

Biochemistry (41 decks)

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