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MCAT Biochemistry > 2. Genetic Code > Flashcards

2. Genetic Code Flashcards

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MCAT flashcards
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

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

Transcription: Initiation

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?

A

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

23
Q

Transcription: Elongation

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)

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
Q

Where does the TATA box (where RNA Pol II) usually fall?

A

~ -25 (upstream of coding region)

26
Q

Transcription: Termination

A
  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
Q

Post-transcriptional Processing

A
  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
Q

Purpose of 5’ cap and Poly-A tail?

A
  • 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
Q

Splicing

A
  • 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
Q

What is the correct sequence of eukaryotic mRNA production?

A
  • Transcription from DNA in nucleus
  • Post-transcriptional processing in nucleus
31
Q

Prokaryotic Ribosome vs Eukaryotic Ribosome

A

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
Q

3 binding sites in the ribosome for tRNA

A

A site: aminoacyl

P site: peptidyl

E site: exit

33
Q

Comparison of DNA polymerase and RNA polymerase

A
34
Q

Compare Eukaryotic and Prokaryotic translation

A

Prokaryotic translation: ribosomes might start translating before mRNA is complete

Eukaryotic: transcription and translation occur @ separate times @ separate locations

35
Q

Translation: Initiation

A

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
Q

What amino acid does Prokaryotes lay down first in initiation step of translation?

A

N-formylmethionine

37
Q

Shine-Dalgarno sequence

A

The site of initiation of translation in prokaryotes

38
Q

What players are involved in Initiation of Translation?

A
  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
Q

Translation Elongation

A

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
Q

Translation: Termination

A

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
Q

Posttranslational processing

A
  • folding by chaperones
  • formation of quaternary structure
  • cleavage of proteins or signal sequences
  • covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
42
Q

What is the effect of exposing a cell to a chemical that inhibits ribosome movement?

A

prevents effective protein synthesis

43
Q

Transcription factors

A

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
Q

Promoter region

A
  • 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
Q

Enhancer Region

A
  • 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
Q

Modification of chromatin structure affects ability of transcriptional enzymes to access DNA; describe effects of:

histone acetylation

A
  • Histone ACETYLATION → INCREASES gene expression
47
Q

Describe effects of DNA Demethylation on gene expression

A

DNA DE-methylation → INCREASES gene expression

48
Q

What (four) factors increase gene expression?

A
  • enhancers
  • gene duplication (series or parallel)
  • histone acetylation
  • DNA demethylation

MCAT Biochemistry (6 decks)

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