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Micro 265 Fall 2023 > 4.2 -Translation > Flashcards

4.2 -Translation Flashcards

1
Q

what are proteins comprised of ?

A
  • of polymers of a.a connected by peptide bonds.
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1
Q

what are proteins?

A
  • they are polypeptides
  • they are basically strings of a.a in which a single subunit is repeated.
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2
Q

what is the basic structure of an a.a?

A
  • there is an amino group on one end.
  • there is an alpha carbon in the middle.
  • Attached to the alpha carbon is the R group, which varies from a.a and makes each a.a unique.
  • then on the right side is a carboxylic acid group.
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3
Q

where are the peptide bonds?

A
  • they are between the carboxylic acid groups of a.a 1 and the amino group pf a.a 2.
  • a.a 1 (C) — a.a 2 (N)……..
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4
Q

Are proteins directional like RNA and DNA?

A
  • they run form the n-terminus to the c-terminus.
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5
Q

how many a.a are there that make up proteins?

A
  • there are 20 a.a
  • they have a different R groups.
  • they all have the same backbone
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6
Q

what are the two rare a.a?

A
  1. selenocysteine
  2. pyrrolysine

-rarely used and only present in certain organisms.

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7
Q

what are the 4 groups a.a can be grouped in?

A
  1. Nonpolar –> hydrophobic (broken down into smaller and larger R groups.)
  2. polar
  3. positively charged
  4. negatively charged
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8
Q

what are the 4 stages of a protein?

A
  1. Primary
  2. Secondary
  3. Tertiary
  4. Quaternary
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9
Q

what is the primary structure?

A

the chain of a.a in a protein.

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10
Q

what is a second structure?

A
  • a chain of polypeptides that forms alpha helixes and beta sheets.
  • the alpha helixes and beta sheets are formed by hydrogen bonding in the peptide backbone (amide H and carbonyl O)
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11
Q

what happens in alpha helixes?

A
  • the hydrogen bonding of the
    C=O —-H-N lines up and forms the helixes.
  • C=O —-H-N is along the axis of the helix
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12
Q

what happens in beta sheets?

A
  • a string of a.a lining beside another a.a

-C=O —-H-N are are horizontally lined up alternatively.

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13
Q

what is a tertiary structure?

A
  • the full 3d structure of a protein
  • Will
    typically include multiple secondary structure elements arranged in
    different ways & other structural features as well
  • can have disulphide bridges and loops.
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14
Q

what is a quaternary structure?

A
  • creates multimeric proteins.

-diff subunits (each has a 3* structure) comes to make a multimeric structure.

  • is the result of multiple polypeptides coming together.
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15
Q

what is a subunit?

A

o The individual polypeptide chains in a multimeric protein

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16
Q

what is a homomeric subunit?

A

same polypeptide chains and all subunits are the same.

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17
Q

what is a heteromeric subunit?

A

different polypeptide chains

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18
Q

What are domains?

A
  • proteins contain them. (most contain a few diff domains)
  • it is a structure formed that carries out some function.
  • they can be large of small
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19
Q

what is an example of a domain?

A
  • “helix-turn-helix” (HTH) domains
  • HTH domains bind DNA – found in >200
    different proteins in any given Salmonella
    genome…mostly DNA-binding regulatory
    proteins.
  • each protein will have different domain that carry different functions
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20
Q

what is a tRNA?

A
  • it reads the code in RNA and then converts it to a specific language of a.a
  • the ribosome uses tRNA to convert the mRNA sequence into a protein sequence.
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21
Q

what do tRNAs often contain?

A
  • they contain modified bases, which is residues that are chemically altered after transcription
  • modify to give friendly bases
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22
Q

what does each tRNA have?

A
  • it has a specific anticodon that binds a particular three-base condon.
  • At other end, tRNAs carry the specific
    amino acid (cognate amino acid) that
    corresponds to that codon.
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23
Q

what is a tRNA synthetase?

A
  • are the enzymes that
    “charge” tRNAs – add the amino
    acid to the CCA at the 3’ end
  • it basically corrects a.a to recharge the codon.
24
Q

Explain the tRNA structure and how it works?

A
  • at the bottom we have a codon sequence from 5’ to 3’, and on the sequence is a codon.
  • the bottom part of the tRNA has an anticodon which will read the sequence of RNA and will try to match the base pairs.
  • on the top of the tRNA structure that matchs up with the base pair
25
Q

Does each genetic codon correspond to an a.a?

A
  • Each codon corresponds to a specific amino acid, or to a stop codon.
  • There are 64 possible codons and 20 amino acids – multiple different
    codons can encode a particular amino acid
  • Sometimes there is a distinct tRNA for each codon that encodes a given
    amino acid
26
Q

Can tRNA work is there is a mismatch in the 3rd position?

A
  • it can still work.
  • the mismatch in the position is called a WOBBLE (same tRNA for 2 diff codons).
  • let’s say we have a UUU and a UUC. we can tell that the third position varies.a. however we know that the third position i flexibel and doesn’t care if it is a U or C
27
Q

What is the start codon?

A
  • encodes the first a.a
  • a specific codon that tells the ribosomes to start.

-Where translation begins. It is
typically an AUG (ATG in DNA sequence) for all three domains of life

28
Q

what are the alternative start codons?

A
  • they can be used in bacteria, such as e.coli
  • it is GUG, UUG
29
Q

what is the start codon translated to in bacteria?

A
  • start codon is translated to N-formylmethionine (fMet)
    (chemically modified version of methionine) using a special tRNA.
  • it puts fMet regardless of which a.a is coded with the codon. Is then removed after translation
30
Q

when is unmodified methionine used?

A
  • used in archaea and eukarya.
31
Q

what are the three stoop codons?

A
  • UAA, UGA & UAG
  • it doesn’t code for any a.a but tells ribosome to stop
32
Q

what is the prokaryote ribosome?

A
  • it is the 70S
  • it is made up of two subunits.
  • half of it is 30S (small subunit)
  • the other half is a 50S (large subunit)
  • each of the subunits are comprised of rRNA and ribosomal proteins.
33
Q

how do 30s and 50s interact during translation?

A
  • interact dynamically
34
Q

what is an example of a ribosome?

A
  • E. coli 30S ribosome contains 16S (just in one half) rRNA & 21 proteins.
  • 50S contains
    5S/23S rRNA (in the other half ) and 31 proteins.
  • Ribosomes are large, complex machines.
35
Q

what is the main function of rRNA?

A
  • carries out much of the main function of
    ribosome – including catalyzing peptide bond
    formation
36
Q

How is a start codon indicated in an RNA?

A
  • by the ATGs and the Ribosome binding site.
  • there are lots of ATGs, and using this we want to make it start in the right place.
  • there are also a ribosome binding site (RBS), which also tells us where we will start.
  • together the spacing between ATG and RBS, determines a good spot for translation.
  • 16S rRNA component of a free 30S ribosomal subunit (not bound to 50S)
    binds to RBS/start codon to initiate translation.
37
Q

what happens after a good place is found?

A
  • Initiator (fMet) tRNA then binds the start codon.
    a. interacts with a 30s ribosome and has a fMet. Energy (GTP is the core energy) use to bring in the other half of ribosome.
  • Once bound, energy from
    GTP is used to recruit 50S subunit & full 70S ribosome forms.
38
Q

what is the next step after initiation?

A
  • elongation
39
Q

what 3 tRNA binding sites are there?

A
  1. A (aminoacyl) site
  2. P (peptidyl) site
  3. E (exit) site
40
Q

what is A (aminoacyl) site?

A
  • Where new charged tRNAs enter and recognize the
    codon being translated.
  • Once in place, the growing peptide from P site is
    transferred its amino acid & peptide bond forms.
41
Q

what is the P (peptidyl) site?

A
  • After peptide bond formation, translocation occurs –
    RNA moves 3 bases (one codon).
  • The tRNA from A site moves to P site.

-This tRNA transfers growing amino acid chain to the new charged tRNA
that has entered the A site.

-P site tRNA now lacks amino acid (uncharged)

42
Q

what is the E (exit) site?

A
  • Uncharged tRNAs exit here
43
Q

steps of translation?

A
  1. codon recognition

a. in the p site there is already an indicator and its first amino acid is attached to the top of tRNA.

b. in the A site there is a codon, which matches up with the next tRNA codon. The tRNA will come and will recognize the codon.

  1. peptide bond formation

a. through the use of energy as GTP the peptide bond is formed between the two a.a.

b. this will cause first a.a to be transferred to the second.

  1. Trasnlocation (requires EF-Tu and EF-Ts. )

a. The tRNA moves and shifts one over.

  1. cycle continues three time, or until ribosome encounters a stop codon.

a. Once this occurs, a protein called a release factor binds – releases
peptide and mRNA – 30S/50S dissociate.

b. Ribosome free to begin again.

44
Q

what are polysomes?

A
  • The same mRNA can be simultaneously translated by multiple different
    ribosomes – multiple ribosomes on a single transcript
45
Q

Translation in Prokaryote?

A
  • As 5’ end of RNA in an ORF is translated & freed up, a new ribosome
    can bind and begin making protein before the previous ribosome is finished
  • each ribosome on a polysome builds a complete protein.
46
Q

are translation and transcription coupled in prokaryotes?

A

– RNA being translated while transcription still going
on (RNA polymerase and ribosomes both attached to transcript)

47
Q

key point about translation?

A
  • every organism that does this but differs in how they do it.
  • bacteria –> multiple
    a. not in eukaryotes.
  • mechanistically diff in initiation step for prokaryotes and eukaryotes
48
Q

is eukaryotic translation a conserved process?

A

True

49
Q

Is transcription or translation coupled in eukaryotes?

A
  • occur in diff compartments.
  • transcription occurs in the nucleus and translation in the cytoplasm.
  • they are both separated by time and location.
50
Q

how many does each eukaryotic mRNA encode for?

A
  • one gene
51
Q

how many does each prokaryotic mRNA encode for?

A
  • encode 2+ ORF
    a. portion of a DNA sequence that does not include a stop codon (open reading frame –> ORF)
  • ribosomes initiate on same transcript
52
Q

what is the main mechanistic diff in eukaryotes and prokaryotes?

A
  • initiation step
  • 5’ cap recognized
    by initiation complex in eukaryotes (ribosome binding site).
  • More
    regulation/complexity at this step.
53
Q

Are eukaryotic ribosomes larger?

A
  • Eukaryotic ribosomes are larger and a bit more complex - 40S (small
    subunit)/60S (large subunit).
  • 80S complete ribosome
54
Q

what are chaperons?

A
  • are proteins that help other proteins adopt their properly
    folded and fully active state - all 3 domains in life require chaperones.
  • many can fold in a 3D structure. but many require chaperones
  • they also help multimeric proteins to come together.
55
Q

what is the function of a chaperon?

A
  • initial folding, re-folding denatured proteins, helping
    subunits in multimeric proteins come together, preventing aggregation,
    incorporating cofactors into enzymes…there are even RNA chaperones
  • proeteins are usually folded in a tigth structure, but may have a floppy structure and this si recognized by the chaperon and then which tightens it and creates a stable environment for the protein.
56
Q

what do chaperons use?

A
  • ATP hydrolysis.

-The precise mechanisms are complex
(and still subject to debate in many cases).

  • But they commonly enable
    unfolded or unstable conformations to re-fold in a controlled fashion
57
Q

when are special chaperons activated?

A
  • are activated in response to high or low temperatures
    (heat shock / cold shock proteins) to assist with protein/RNA folding

Micro 265 Fall 2023 (9 decks)

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