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BIOL 130 Midterm > Unit 4B > Flashcards

Unit 4B Flashcards

1
Q

Genetic Code

A
  • relationship between sequence of nucleotides in DNA / RNA and sequence of amino acids in a protein
  • 64 (4^3) possible codons yet only 20 amino acids (AAs)
  • all AAs except methionine (Met) and tryptophan (Trp) specified by more than one codon, but one codon never specifies more than one AA
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2
Q

Genetic code pt 2

A
  • for AAs with multiple codons, third base is most variable
  • genetic code is almost universal
  • same codons assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microbes
  • exceptions: some fungi and protozoa; mitochondria
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3
Q

Exceptions to Genetic Code

A

common exception is to assign some of the three STOP codons to an amino acid
exceptions in mitochondria:
- e.g. mitochondria from animal cells use UGA to encode tryptophan (rather than STOP)
has implications for transferring of mitochondrial genes to nuclear genome
- cytosolic protein- synthesizing machinery reading a mitochondrial gene will always STOP when it should be inserting a tryptophan!

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4
Q

Genetic Code and Reading Frame

A
  • loss or gain of bases (deletions, insertions) that shift the reading frame (frame shift mutations) can lead to novel proteins that are beneficial, or they can be disastrous …
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5
Q

Redundancy in the Genetic Code and tRNAs

A
  • several different codons can specify the same AA
    what about the specificity of tRNAs?
  • some AAs have more than one tRNA
  • some tRNAs need accurate base-pairing at only the first two bases of a codon
  • can tolerate mismatch (‘wobble’) at third position
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5
Q

How does an mRNA codon specify an amino acid?

A
  • Francis Crick proposed that an ‘adapter molecule’ held amino acids in place while interacting directly and specifically with a codon in mRNA.
  • Transfer RNA is the Adapter
  • each amino acid has its own aminoacyl tRNA synthetase
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6
Q

wobble hypothesis:

A

the anticodon of tRNAs can still bind successfully to a codon whose third position requires a nonstandard base pairing

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7
Q

Loading tRNA with amino acid: aminoacyl-tRNA synthetase

A
  • total of 20 aminoacyl-tRNA synthetases
  • each synthetase must recognize its amino acid plus all anticodons that recognize that amino acid
  • hydrolysis of ATP will be coupled to attachment of amino acid to tRNA
  • combined action of tRNA and synthetases ensures that each mRNA codon is matched to correct amino acid
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8
Q

‘charging’ of tRNA (e.g. tRNA specific to leucine)

A
  1. active site binds ATP & amino acid
  2. leucine bound to AMP now ‘activated
  3. activated amino acid
    transferred to tRNA (tRNA specific to leucine)
  4. finished aminoacyl tRNA
    ready for translation
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9
Q

Components of Ribosomes (eukaryotic)

A

large subunit:
catalyzes formation of peptide bonds
small subunit:
matches tRNAs to codons

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10
Q

Overview of Mechanism of Translation

A

translation begins …
- when the anticodon of a ‘charged’ tRNA binds to a codon in mRNA
translation ends …
- when that amino acid forms a peptide bond with growing chain

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11
Q

Translation: Initiation

A
  • The small ribosomal subunit binds to the mRNA molecule
  • The initiation complex forms when the initiator tRNA carrying methionine binds to the start codon (AUG) on the mRNA
  • Then, the large ribosomal subunit joins the complex, forming a functional ribosome.
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12
Q

Translation: Translocation

A
  • After each peptide bond formation, the ribosome advances to the next codon along the mRNA, causing the ribosome to move relative to the mRNA
  • This movement shifts the tRNAs from the A (aminoacyl) site to the P (peptidyl) site and then to the E (exit) site
  • The tRNA is released from the E site, and the process repeats as the ribosome moves to the next codon.
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13
Q

Translation: Elongation

A
  • the ribosome moves along the mRNA, reading the codons one by one.
  • Aminoacyl-tRNA molecules carrying specific amino acids enter the ribosome, and their anticodons base-pair with complementary codons on the mRNA
  • Peptide bonds form between adjacent amino acids, creating a growing polypeptide chain
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14
Q

Translation: termination

A
  • When a stop codon (UAA, UAG, or UGA) is encountered on the mRNA, it signals the termination of protein synthesis
  • Release factors bind to the stop codon, causing the ribosome to release the completed polypeptide chain
  • The ribosome subunits dissociate from the mRNA, and the newly synthesized protein is released into the cytoplasm for further processing or targeting to its functional location.
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15
Q

what is a release factor in translation

A

alters catalytic activity, causing addition of a water rather then forming a peptide bond

16
Q

Is the ribosome an enzyme or a ribozyme?

A
  • A, P and E sites are primarily rRNA
  • catalytic site where peptide bond is formed between P and A sites in large subunit is formed entirely by RNA, not protein
  • ribosomal proteins are mostly on surface, helping to create and maintain shape of RNA core
17
Q

ribozyme definition

A

RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction

18
Q

Proteins are made on polyribosomes (polysomes).

A
  • takes from 50 sec to 1-2 mins for a single ribosome to translate a protein
  • output can be greatly increased if another ribosome hops on the mRNA and starts translating the same message as soon as the first one is out of the way
  • common in both bacteria and eukaryotes
19
Q

tetracycline

A

blocks binding of aminoacyl-tRNA to a A site of ribosome

20
Q

streptomycin

A

prevents the transition from initiation complex to chain elongation, causing miscoding

21
Q

chloramphenicol

A

blocks the peptidyl transferase reaction on ribosomes

22
Q

cycloheximide

A

blocks the translocation step in translation

23
Q

rifamycin

A

blocks initiation of transcription by binding to and inhibiting RNA polymerase

24
Q

When do proteins fold?

A
  • folding begins during translation, long before termination and disassembly of ribosomes
  • assisted by proteins called molecular chaperones
  • some chaperone proteins bind to ribosome near ‘tunnel’ where growing peptide exits
25
Q

Post-Translational Modifications (PTMs

A
  • chemical modification of protein structure (modification of the original 20 amino acids)
  • generally involves addition of functional groups or small molecules

BIOL 130 Midterm (4 decks)

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