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MCAT Biochemistry > 2. Genetic Code > Flashcards

2. Genetic Code Flashcards

(48 cards)

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1
Q

Are spliceosomes the only thing that can cause splicing?

A

No, there are other nonspliceosome that can allow for splicing during post-transcriptional processing

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2
Q

Central dogma of molecular biology

A
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3
Q

Describe the mRNA of eukaryotes? Prokaryotes?

A

Eukaryotes: monocistronic (1 mRNA → 1 protein)

Prokaryotes: polycistronic (1 mRNA → multiple proteins)

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4
Q

Monocistronic

A

Means that 1 mRNA codes for 1 protein

(e.g. Eukaryotic mRNA)

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5
Q

tRNA

A

transfer RNA is a folded strand of RNA that contains a 3-nucleotide anticodon that pairs w/ the appropriate mRNA codon during translation, and is charged w/ the corresponding amino acid

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6
Q

rRNA

A

ribosomal RNA: is the structural and enzymatic RNA found in ribosomes that takes part in translation

KCs:

  • synthesized in nucleolus
  • major component of ribosome
  • may function as ribozymes (RNA molecule w/ enzymatic activity)
  • catalyze peptide bond formation
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7
Q

Codons

A

3-nucelotide sequence in an mRNA molecule that pairs w/ an appropriate tRNA anticodon during translation

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8
Q

What are the start codon(s)?

A

The first codon in an mRNA molecule that codes for an amino acid

AUG (methionine)

*All mRNA starts w/ Methionine or N-formul-methionine

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9
Q

What are the stop codon(s)?

A

The last codon of translation; release factors bind here, terminating translation

  • UAA
  • UGA
  • UAG
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10
Q

Types of mutations. Which is most severe?

A
  • Silent
  • Missense
  • Nonsense
  • Frameshift* most severe because it affects the entire rest of the protein; has greatest effect
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11
Q

Silent mutation

A

mutation in wobble position of a codon or noncoding DNA that leads to no change in the protein produced during translation

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12
Q

Missense mutation

A

Mutation in which one amino acid is substituted for by a different amino acid

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13
Q

Nonsense mutation

A

Mutation in which a coding codon is changed to a STOP codon; also called “truncation mutation”

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14
Q

Frameshift mutation

A

A change in DNA in which the reading frame of the codons in mRNA is shifted due to the insertion or deletion of nucleotides (other than in multiples of 3)

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15
Q

Which mutation does NOT result in change to encoded peptide?

A

Silent

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16
Q

Naming convention of peptides

A

When naming N-terminus → C-terminus,

you name 5’ → 3’

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17
Q

Difference between (1) silent/missense/nonsense and (2) frameshift mutations?

A

Silent/missense/nonsense involve only a SINGLE BASE CHANGE

Frameshift mutation involves +/- bases; so there is a whole new amino acid sequence or a premature STOP codon

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18
Q

Mechanism of transcription (high level)

A
  1. Unwinding to prevent supercoiling, involves helicase and topoisomerase enzymes
  2. Reads template strand (anti-sense) from 3’ → 5’
  3. Newly synthesized strand is antiparallel and complementary to the DNA template strand
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19
Q

3 types of DNA polymerase (location, function)

A
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20
Q

Steps of Transcription

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A
  1. Initiation
  2. Elongation
  3. Termination
21
Q

Transcription: Initiation

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A
  1. Uses DNA-dependent RNA polymerase
  2. RNA polymerase searches for promoters
    • transcription factors help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start

In eukaryotes, RNA Pol II binds to TATA box (named for the conc. of A and Ts)

22
Q

Does RNA polymerase require a primer?

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A

NO! DNA replication needs a primer, but RNA polymerase does NOT

23
Q

Transcription: Elongation

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A
  1. RNA Pol travels along template strand in 3’ → 5’ direction
  2. Transcript is generated in 5’ → 3’ direction
  3. Does not proofread
  4. Since coding (sense) strand of DNA is NOT used during transcription, it is complementary to template and therefore IDENTICAL to the mRNA transcript (except T → U)
24
Q

Naming convention (downstream vs. upstream)

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A

Start w/ first base transcribed from DNA → RNA, defined as +1 base

Upstream (left, towards 5’ end) are given negative numbers

Downstream (right, toward 3’ end) are denoted w/ positive numbers

25
Where does the TATA box (where RNA Pol II) usually fall?
~ -25 (upstream of coding region)
26
Transcription: Termination
1. Continues until RNA polymerase reaches a **termination sequence** or **stop signal**, which results in termination 2. DNA double helix reforms 3. primary transcript formed is termed heterogenous nuclear RNA (hnRNA), mRNA is derived from hnRNA via posttranscriptional modifications
27
Post-transcriptional Processing
1. capping (**5' cap**) and **poly-A tail** (@ 3' end) 2. **splicing** by spliceosomes (snRNA and snRNPs in the nucleus * (excised intron [lariat] degraded in nucleus 3. **transport** to cytoplasm and translation
28
Purpose of 5' cap and Poly-A tail?
* **5' cap:** (**7-methylguanylate triphosphate cap)**; added during transcription & is recognized by ribosome @ binding site; protects mRNA from degradation * **Poly-A tail**: (polyadenosyl [poly-A] tail) is added to 3' end of mRNA transcript and protects the message against rapid degradation; * longer the poly-a tail, the longer the mRNA will be able to survive before it is digested * assists w/ export of mature mRNA from nucleus
29
Splicing
* Post-translational modification * Contributes to diversity of proteins that can be made from single DNA/RNA * Introns can be spliced out (lariats are degraded), and coding exons are kept
30
What is the correct sequence of eukaryotic mRNA production?
* Transcription from DNA in nucleus * Post-transcriptional processing in nucleus
31
Prokaryotic Ribosome vs Eukaryotic Ribosome
Ribosome is composed of proteins and rRNA; both have large and small subunits that ONLY bind together during proteins synthesis **Prokaryotic**: 50S + 30S = **70S\*** **Eukaryotic**: 60S + 40S = **80S**\* *\*the S values are not additive bc they are based on shape and size, not size alone*
32
3 binding sites in the ribosome for tRNA
A site: aminoacyl P site: peptidyl E site: exit
33
Comparison of DNA polymerase and RNA polymerase
34
Compare Eukaryotic and Prokaryotic translation
Prokaryotic translation: ribosomes might start translating before mRNA is complete Eukaryotic: transcription and translation occur @ separate times @ separate locations
35
Translation: Initiation
**Prokaryotes**: occurs when 30S ribosome attaches to the Shine-Dalgarno sequence and scans for start codon; lays down N-formylmethionine in P site of ribosome **Eukaryotes**: when 40S attaches to 5' cap and scans for start codon; lays down Methionine in P site of ribosome
36
What amino acid does Prokaryotes lay down first in initiation step of translation?
**N-formyl**methionine
37
Shine-Dalgarno sequence
The site of initiation of translation in prokaryotes
38
What players are involved in Initiation of Translation?
1. Ribosomal subunit binds/scans mRNA 2. Charged **initiator tRNA** binds to AUG start codon thru base pairing w/ its anticodon w/in P site 3. Large subunit binds to small subunit → forming completed initiation complex * Assisted by **initation factors** (IF) that are not permanently associated w/ the ribosome
39
Translation **Elongation**
involves addition of new **aminoacyl-tRNAs into the A site** of ribosome, transfer of growing polypeptide chain from the tRNA in the P site to the tRNA in the A site; the now uncharged tRNA pauses in the E site before exiting ribosome
40
Translation: Termination
occurs when the codon in the A site is a STOP codon; **release factor** places a water molecule on the polypeptide chain and thus releases it from protein
41
**Posttranslational** processing
* folding by **chaperones** * formation of **quaternary** structure * **cleavage** of proteins or signal sequences * **covalent addition** of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
42
What is the effect of exposing a cell to a chemical that inhibits ribosome movement?
prevents effective protein synthesis
43
Transcription factors
proteins that search for promoter and enhancer regions in the DNA; specifically help RNA Pol II locate and bind to these regions Types: *promoters, enhancers*
44
Promoter region
* w/in 25 bps of the transcription start site * portion of DNA upstream from a gene; contains the TATA box, which is the site where RNA Pol II binds to start transcription
45
Enhancer Region
* greater then 25 base pairs from transcription start site * A collection of several response elements that allow for the control of one gene's expression by multiple signals
46
Modification of chromatin structure affects ability of transcriptional enzymes to access DNA; describe effects of: ## Footnote **histone acetylation**
* Histone **ACETYLATION** → **INCREASES** gene expression
47
Describe effects of **DNA Demethylation** on gene expression
DNA DE-methylation → INCREASES gene expression
48
What (four) factors increase gene expression?
* enhancers * gene duplication (series or parallel) * histone acetylation * DNA demethylation

MCAT Biochemistry (6 decks)

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