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Pharm 411: fundamentals of molecular bio > Pharm 411: The genetic code and Protein Synthesis > Flashcards

Pharm 411: The genetic code and Protein Synthesis Flashcards

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1
Q

What is the tRNA do?

A

its the link between the two codes (DNA code and RNA code) since it carries the amino acid to the site of protein synthesis

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2
Q

How do you read mRNA?

A

ALWAYS from the 5’ to 3’ and the growing protein chain ALWAYS GROWS from the N-terminal residue

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3
Q

What is the basic unit of genetic code?

A

The codon; which is a group of three nucleotides, found in mRNA

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4
Q

What is the anticodon?

A

Part of the tRNA which has three bases and pairs with codon

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5
Q

What is a start codon?

A

signals the start of the protein and codes for the first amino acid (n-terminus) AUG

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6
Q

What is a stop codon?

A

End of protein synthesis UAA UAG UGA

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7
Q

Why do amino acids come in groups of three?

A

With only 4 bases, they wouldnt be able to code for all 20 amino acids alone, and two bases together could only code for 16 Using 3 bases means 61 codons specify an amino acid with 3 stop codons

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8
Q

What does it mean by amino acids are degenerate?

A

It means that amino acids often have more than one possible codon

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9
Q

What is a open reading frame?

A

Codons are read from a fixed starting position, three nucleotides at a time in the 5’-3’ direction. The reading frame starts with a start codon and then ends with an end codon

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10
Q

Do we use overlapping or non-overlapping code?

A

We use non-overlapping (we always read in sections of 3)

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11
Q

What are the two types of mutations and what occurs with each?

A

Point mutation: change in ONE base with no effect on reading frame Frameshift mutation: One or two nucleotide insertion or deletion moves the reading frame out of register, which will give a shorter or longer protein with different protein sequence

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12
Q

What are the different types of point mutations?

A

Silent missense nonsense

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13
Q

What is a silent mutation?

A

Change in codon does not result a change in the amino acid sequence uUG-(leu) —> cUG (leu)

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14
Q

What is a missense mutation?

A

Change in codon results in change in amino acid sequence UuG (leu) —-> UcG (ser)

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15
Q

What is a nonsense mutation?

A

Change in codon results in a premature stop codon UuG - (leu) —-> UaG (stop) leads to smaller protein

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16
Q

What can the result of mutations give?

A

A mutation could be positive, negative or neutral There is no way to know what effect a mutation will have but the majority of the time they will have a negative effect

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17
Q

What is an insertion mutation?

A

Frameshift When you insert one or two base pairs into the mRNA which will cause a shift in the reading frame

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18
Q

What is a deletion mutation

A

Frameshift When you delete a section of the mRNA and it shifts your reading frame

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19
Q

What does is meant by charging tRNA?

A

Its the process where an amino acid is attached to tRNA which will form an amioacyl-tRNA

20
Q

Where is the amino acid added onto the tRNA?

A

Its attached on the 3’ end of tRNA

21
Q

What is responsible for charging tRNA?

A

aminoacyl-tRNA synthetases Each synthetase is specific for one amino acid and for one or more tRNA

22
Q

Why is it important to have high specificity for amioacyl-tRNA synthetases?

A

to build the correct protein its very important to have the tRNA to have the correct amino acid attached so it can translate the genetic code to a protein

23
Q

Where do edits of tRNA changing take place?

A

They happen within the synthetase; once the tRNA leaves the synthetase there is no way we can edit it or check it for accuracy.

24
Q

How does the aminoacyl-tRNA synthetases make sure that it binds the correct amino acids?

A

It has an editing site as well as an acylation site -The acylation site will reject amino acids that are larger than the correct one -The editing site rejects amino acids that are smaller than the correct one **all the editing happens without dissociation of the tRNA from the synthetase

25
Q

What does the term wobble mean?

A

Used for pairing between two nucleoti that do not follow watson-crick base pairing rules These is the reason for the last codon is most often different and why amino acids have degeneracy

26
Q

What is the wobble position?

A

Base pairing between the first nucleotide of tRNA (5’ end) and the third nucleotide of the mRNA codon (3’ end) **ALWAYS AT 5’ end of anticodon

27
Q

What causes the formation of inosine?

A

the deamination of adenine

28
Q

What are the 5 bases involved in wobble?

A

Inosine, Guanine, Uracil, Adenine and cytosine

29
Q

What are the base pairings that happen during wobble>

A

Inosine can bind to every thing but guanine guanine can bind to uracil I-C I-U I-A G-U **they can also form their normal bonds

30
Q

EX of wobble 3’ UCG 5’ (anticodon) what are the combos that can happen?

A

(codon) 5’ AGC 3’ U

31
Q

What are the subunits of the ribosome?

A

The large subunit The small subunit

32
Q

What does the large subunit of the ribosome do?

A

It catalyzes the formation of the peptide bonds (it has catalytic rRNA)

33
Q

What does the small subunit of the ribosome do?

A

It binds the mRNA and is responsible for accurate translation by ensuring correct initiation and base pairing

34
Q

How many and what are the sites of the ribosome?

A

It has 4 sites mRNA binding (small subunit) site A (aminoacyl) site P (peptidyl) site E (exit) site

35
Q

What is the A site of the ribosome?

A

The aminoacyl site. this is the site where the aminoactyl-tRNA (charged tRNA) binds

36
Q

What is the P site of the ribosome?

A

the peptidyl site. This is where the growing peptide chain goes

37
Q

What is the E site of the ribosome?

A

Site which is where the uncharged tRNA ends up after transferring the peptide chain to the new amino acid, and where the tRNA leaves the ribosome

38
Q

What happens during prokaryotic initiation of transcription?

A
  1. initiation factors bind to small subunit and help to locate the Shine-Delgarno sequence in the mRNA (upstream from the start codon of mRNA) 2. The small subunit will bind to the Shine-Delgarno sequence which aligns the ribosome for translation 3. The aminoacytl-tRNA for formyl-methionine (fMet) binds to the start codon 4. the large subunit binds with the fMet-tRNA located in the P site forming the complete ribosome
39
Q

What happens during prokaryotic elongation?

A
  1. The next tRNA binds to the codon in the A site 2. The ribosome catalyzes the formation of the peptide bond transferring the amino acid (or peptide chain) in the P site onto the amino acid in the A site 3. The ribosome then shifts down the mRNA (translocation) moving the new peptide-tRNA complex from the A site into the P site 4. The empty tRNA is ejected out of the E site 5. this repeats until a stop codon is encountered
40
Q

What happens during termination of prokaryotic translation?

A
  1. when the stop codon is transloacted to the A site, the synthesis pauses since no tRNA match 2. These stop codons are recognized by release factors which bind to the A-site 3. they hydrolyze the terminal peptideyl bond releasing the polypeptide 4. They also hydrolyze the GTP which breaks apart the ribosome and causes it to dissociate from the mRNA
41
Q

What are the differences between prokaryotic and eukaryotic translation

A
  1. We have larger ribosomes 2. Our initiation step is more complex and needs more protein factors 3. The small ribosomal subunit binds to the 5’ cap and scans down the mRNA for the first AUG codon 4. Our AUG codes from methionine (met) not fMET
42
Q

What do tetracyclines do?

A

Bind to small subunit of ribosome Interfere with tRNA binding (block attachment of tRNA to ribosome) meds = doxycycline and minocycline

43
Q

What do aminoglycosides do?

A

Bind to small subunit of ribosome Bend mRNA and cause misread of codon; blocks initiation and ribosome formation Drug ex: tobramycin and gentamicin

44
Q

What do macrolides do?

A

Bind to large subunit of ribosome Block translocation Drugs: Clarithromycin, erythromycin and azithromycin

45
Q

What do lincosamides do?

A

Bind to large subunit of ribosome Blocks peptide bond formation and translocation Drugs: clindamycin and lincomycin

46
Q

What do Oxazolidinones do?

A

Bind large subunit of ribosome Interferes with initiation and ribosome formation Drugs: linezoild

47
Q

What do amphenicols do?

A

Bind large subunit of ribosome Block peptide bond formation drug: chloramphenicol

Pharm 411: fundamentals of molecular bio (9 decks)

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