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Genetics > M1 L7: Translation and Genetic Code > Flashcards

M1 L7: Translation and Genetic Code Flashcards

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1
Q

Bond between amino acids

A

Covalent, peptide bond

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2
Q

Biological pH amino acid zwitterion

A

molecule with +/- charges but no net charge

ammonium ~NH3+ and carboxylate ~COO-

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3
Q

What part of the ribosome makes the peptide bond

A

peptidyl transferase enzyme (ribozyme)

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4
Q

What are proteinogenic amino acids? How many are there? What’s the significance of non-proteinogenic amino acids? Example of one?

A

Amino acids found in biological proteins

20

Non-proteinogenic AAs have R groups similar to proteinogenic AAs –> cell may incorporate them into a polypeptide but they don’t function the same –> toxic

Canavanine

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5
Q

What are the ends of polypeptides? What ends of mRNA do they associate with?

A

N terminus –> 5’ end
C terminus –> 3’ end

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6
Q

Difference between a polypeptide and a protein?

A

Polypeptide = chain of many amino acids –> one polypeptide can be a protein

protein = functional structure (sometimes many polypeptides)

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7
Q

4 levels of protein organization and relevant bonds?

A

primary: sequence of amino acids, covalent peptide bonds

secondary: hydrogen bonding pattern of backbone (alpha helices or beta sheets), hydrogen bonds

tertiary: 3D shape after folding the polypeptide, ionic, covalent, hydrophobic

quaternary: 3D shape of many folded polypeptides (same forces)

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8
Q

What is protein structure ultimately defined by?

A

primary structure (sequence of AAs)

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9
Q

What are ribosomes made of?

A

rRNA and proteins

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10
Q

Ribosomes provide an environment for…

A

Peptide bond formation

Base pairing between mRNA and tRNA (codons and anticodons)

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11
Q

What direction to ribosomes read in? Where do they start and stop?

A

5’ to 3’ from start codon to stop codon

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12
Q

Purpose of the 5’ and 3’ UTRs?

A

Information for translation initiation and termination

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13
Q

Number of possible polypeptide sequences if n is the number of amino acids

A

20^n

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14
Q

3 key functions of ribosomes

A

bind mRNA and find start codon

facilitate mRNA/tRNA base pairing

catalyze peptide bond formation

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15
Q

What are the channels in the ribosomal subunits for?

A

Small subunit channel for mRNA

Large subunit channel for nascent polypeptide chain

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16
Q

How are rRNAs characterized?

A

Svedberg units (S)

  • roughly proportional to size but not additive (S of small + S of large ≠ S of whole ribosome)
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17
Q

Cast of characters for bacterial translation initiation

A
  1. mRNA
  2. Small subunit
  3. Large subunit
  4. initiator tRNA with f-met
  5. initiation factors (IF3, IF2, IF1)
  6. GTP
18
Q

Describe the steps of bacterial translation initiation

A

IF3 binds small subunit, helps bind mRNA, prevents large subunit from binding, base pairing between rRNA and Shine Dalgarno seq (3-9 bases upstream authentic start) *preinitiation complex

IF2 (bound to GTP) binds and facilitates initiator tRNA with f-met binding

IFI binds and prevents large subunit from binding

IF2 hydrolyzes GTP to GDP, energy makes large subunit bind

IF3, 2, 1 disassociate; A site open for tRNA

19
Q

Cast of characters for eukaryotic translation initiation

A
  1. eIF1
  2. eIF1A
  3. eIF3
  4. eIF4 (a complex)
  5. eIF5
20
Q

Describe the steps of eukaryotic translation initiation

A

eIF1, 1A, and 3 bind the small subunit and facilitate the next steps *preinitiation complex

initiator with tRNA and met binds

eIF5 binds, helps small subunit bind 5’ cap of mRNA

eIF4 binds, scans 5’ to 3’ for Kozak sequence (contains authentic start)

eIF5 hydrolyzes GTP to GDP, large subunit binds, eIFs disassociate, A site open

21
Q

What’s different about archaean translation initiation? What question does it pose?

A

Some archaea have leaderless mRNA w/o a 5’ UTR

  • ancestral state?
  • did bacteria and eukaryotes gain 5’ UTR or did archaea lose 5’ UTR?
22
Q

Cast of characters for translation elongation

A
  1. mRNA
  2. EPA sites
  3. charged tRNA
  4. EF-Tu bound to GTP
  5. EF-G
23
Q

Describe the steps of translation elongation

A

BIND
1) EF-Tu (bound to GTP) binds to ribosome and helps charged tRNA bind to A site

BOND
2) codon/anticodon pairing between mRNA/tRNA leads EF-Tu to hydrolyze the GTP to GDP, EF-Tu disassociates

peptidyl transferase forms the peptide bond to the nascent chain –> nascent chain on tRNA in A site

MOVE
3) tRNA from P site moves to E, A moves to P, A site open

EF-G moves ribosome 3 bases towards 3’ end

24
Q

Translation termination cast of characters

A
  1. Stop codons
  2. Release factors

Bacteria: RFI, RFII, RFIII

Eukaryotes: eRFI, eRFIII

archaea: aRFI

25
Q

Describe the steps of translation termination

A

No tRNA can decode stop codons

RFI, RFII, eRFI, aRFI (bound to GTP) decode stop codon and bind the A site (bacteria need 2 release factors to decode all 3 stop codons)

Hydrolyze GTP, tRNA in P site releases polypeptide

RFIII, eRFIII help ribosomal subunits disassociate from mRNA (“recycling”)

26
Q

What bacterial release factors decode which stop codons

A

RFI UAG and UAA

RFII UAA, UGA

27
Q

What are polyribosomes

A

complex of many ribosomes which can decode one mRNA at the same time

28
Q

How does the frequency of translation errors compare to transcription? How is this possible?

A

Translation has more errors. This is better tolerated because these mutations aren’t heritable. They only affect that one polypeptide or protein.

29
Q

What are polycistronic mRNAs? What organisms are they most common in?

A

mRNAs with many genes on one transcript (each have own start and stop codons, are separated by intercistronic spacers)

common in bacteria

30
Q

What are some post translational modifications? Why do we need them?

A

Bacteria cleave fmet

eukaryotes cleave N terminal met

phosphorylation, methylation

Important for making the protein functional

31
Q

Why do we need the genetic code?

A

mRNA and amino acids are very chemically different, no great way to turn one into the other

32
Q

Is the genetic code always universal? If there are exceptions, do they pose strong doubt for the single origin of life?

A

No, some organisms have changed the genetic code. Mostly in mitochondria - they have their own genome

Other exceptions are in yeast, all changed CUG (no longer encode for leucine)

Do not pose much doubt for single origin of life theory - changes are very slight. Genetic code mostly universal

33
Q

Describe the different interpretations and actions tRNAs can make

A

interpret base pairing –> bind to A site, hydrolyze GTP, peptide bond

No base pairing –> leave A site, no hydrolysis or prptide bond

34
Q

How can organisms encode 64 codons with less than 64 different tRNAs?

A

1) wobble hypothesis: 3rd base in pairing is relaxed

2) inosine modification: changing 3rd position A in tRNA to I (can ind with A, U, C) –> same tRNA can decode multiple codons

35
Q

What charges tRNA

A

animoacyl tRNA synthetase adds amino acid to 3’ end of tRNA (acceptor stem)

very specific (multiple points of contact for tRNA), one for each of the 20 amino acids, ATP dependent

36
Q

What are isoaccepting tRNAs

A

different tRNAs w/ same AA

37
Q

Why did people think codons were 3 bases?

A

2 bases = 4^2 (4 nucleotides) = 16 codon combos (not enough for 20 AAs)

4 bases = 4^4 = 128 codons (way too many)

3 bases = 4^3 = 64 codons (reasonable)

38
Q

3 questions about genetic code and how they were answered

A

Is it overlapping?
NO - point mutations don’t affect 3 adjacent AAs, no requirements for what AAs must follow each other

Does it have a delimiter? (spacers btwn codons)
NO - insertions/deletions shift whole frame

Is it made of triplets?
YES - 1 insertion/deletion messes up rest of AAs, 3 insertions/deletions near each other realigns rest of codons –> rest of AAs normal

39
Q

H

A
40
Q

How were codons deciphered?

A

In vitro

Decode single nucleotide codons first

Then make all possible codons, do 20 tests with each, each test has 1 tRNA w/ a radiolabeled AA

Add a ribosome, charged tRNAs, codons –> observe which radiolabeled AAs were not present after filtering the contents (tRNA w/ AA still stuck to ribosome, won’t pass through filter)

Genetics (7 decks)

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