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Microbiology 200 > Topic 6-L2- Translation > Flashcards

Topic 6-L2- Translation Flashcards

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Biology 101 flashcards
1
Q

Proteins are _________. They are comprised of polymers of amino
acids connected by __________

A

polypeptides. peptide bonds.

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2
Q

Amino acids have an

A

amino group on one side, an ⍺–carbon in the middle (has “R group”) and a carboxyl group on the other side.

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3
Q

Peptide bonds are between the

A

carboxylic acid group of one amino

acid and the amino group of the next amino acid.

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4
Q

proteins are directional based on how

polymers are assembled

A

from N-terminus (free amino terminus) to C-terminus (free carboxylic acid terminus

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5
Q

There are 20 different amino acids that make up proteins. They have the

A

same backbone, but different R groups.

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6
Q

primary structure

A

The chain (sequence) of amino acids in a protein

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7
Q

secondary structure.

A

Small segments of protein adopt simple local structures (local in 3D space, not necessarily in sequence)

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8
Q

Most common secondary structure elements are

A

⍺-helices & β-sheets. Formed by hydrogen bonding in peptide backbone (amide H & carbonyl O)

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9
Q

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

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10
Q

Quaternary structure is the result of

A

multiple different polypeptides

coming together – multimeric proteins (or protein complexes).

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11
Q

The individual polypeptide chains in a multimeric protein are

A

subunits. Can be:

  • identical (homomeric)
  • different (heteromeric)
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12
Q

Proteins contain “domains” - these are

A

structural and/or functional
segments. Can be small or large - most proteins contain a few (or more)
different domains

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13
Q

A given domain is defined as having a particular

A

structure and/or carrying out a particular function. Typically, a given domain will be found in a number of different proteins.

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14
Q

Common domain example

A

“helix-turn-helix” (HTH) domains

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15
Q

HTH domains bind DNA – found in

A

> 200 different proteins in any given Salmonella genome…mostly DNA-binding regulatory binding proteins.

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16
Q

The ribosome uses tRNAs to

A

convert (“translate”) the mRNA sequence into a protein sequence

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17
Q

Each tRNA has a specific

A

anticodon that binds a particular three base codon.

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18
Q

At other end, tRNAs carry the specific

A 
amino acid (cognate amino acid) that
corresponds to that codon.
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19
Q

tRNA synthetases are the enzymes that

A

“charge” tRNAs – add the amino

acid to the CCA at the 3’ end.

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20
Q

“wobble” –

A

same tRNA for 2 different codons

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21
Q

start codons – mostly

A

AUG, GUG, UUG.

In E. coli:
83% AUG, 14% GUG, 3% UUG.

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22
Q

In bacteria, start codon is translated to

A

N-formylmethionine (fMet)

(chemically modified version of methionine) using a special tRNA.

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23
Q

AUG encountered during normal translation encodes a standard

A

methionine. fMet often removed from proteins after translation.

24
Q

In Archaea/Eukarya, __________ is used

A

methionine (unmodified)

25
Q

The three stop codons are

A

UAA , UGA & UAG

26
Q

Prokaryotic ribosome is the 70S ribosome – is made up of two subunits

A

– 30S (small subunit) and 50S (large subunit). Each subunit is comprised of rRNA and ribosomal proteins.

27
Q

30S & 50S interact dynamically

A

associate/dissociate during translation

28
Q

E. coli has ribosomes like

A
  • 30S ribosome containing 16S rRNA And 21 proteins.

- 50S containing 5S/23S rRNA and 31 proteins.

29
Q

rRNA carries out much of the main function of ribosome – including

A

catalyzing peptide bond formation.

30
Q

For each ORF, bacterial mRNAs contain a

A

ribosome binding site (RBS) also known as a Shine-Dalgarno sequences (with 5’ UTR).

31
Q

The RBS binds to

A

16S rRNA in a free 30S ribosomal subunit (no 50S) – helps ribosome locate bona fide start (typically AUG) codons.

32
Q

Free 30S subunit binds RBS, fMet tRNA binds AUG. Using GTP for
energy, 50S subunit recruited –
_________ forms.

A

full 70S ribosome

33
Q

The ribosome has 3 tRNA binding sites:

A
  • A (aminoacyl) site
  • P (peptidyl) site
  • E (exit) site
34
Q

A (aminoacyl) site:

A

Where new charged tRNAs enter and recognize the codon being translated. Growing peptide from P site is transferred to the amino acid carried by the tRNA. Translocation occurs – RNA moves 3 bases (one codon).

35
Q

P (peptidyl) site:

A

Second position - tRNA moves to P site. Now this tRNA transfers growing amino acid chain to new charged tRNA that has entered the A site. Once complete, tRNA lacks amino acids (uncharged)

36
Q

E (exit) site:

A

Uncharged tRNAs exit here

37
Q

During translation, going through the three RBS repeats until ribosome encounters a stop codon. Once this occurs, a protein called a

A

release factor binds – releases peptide and mRNA – 30S/50S dissociate. Ribosome free to begin again.

38
Q

The same mRNA can be simultaneously translated by multiple different ribosomes – multiple ribosomes on a single transcript called

A

polysomes

39
Q

transcription and translation are often

A

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

40
Q

Each eukaryotic mRNA encodes

A

one gene – contrasted prokaryotic

transcripts encode 2+ ORFs (ribosomes re-initiate on same transcript)

41
Q

Main mechanistic differences in the initiation step. 5’ cap recognized
by

A

initiation complex in eukaryotes (ribosome binding site). More regulation/complexity at this step.

42
Q

Eukaryotic ribosomes are larger and a bit more complex then prokaryotes -

A

40S (small subunit)
60S (large subunit)
80S complete ribosome

43
Q

Chaperones are proteins that help

A

other proteins adopt their properly

folded and fully active state

44
Q

Do all three domains use chaperons?

A

Yes

45
Q

Chaperones functions:

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

46
Q

How do chaperones gain energy?

A

ATP hydrolysis

47
Q

Special chaperones are activated in response to

A

high or low temperatures (heat shock / cold shock proteins) to assist with protein/RNA folding

48
Q

In E. coli major chaperones include

A

DnaJ/DnaK, GroEL and GroES.

49
Q

NarJ is a different sort of chaperone. It inserts an

A

essential cofactor – Moco (contains molybdenum) - in the enzyme nitrate reductase

50
Q

All proteins are synthesized by

A

ribosomes in the cytoplasm

51
Q

All prokaryotes use

A

translocase systems that transport proteins across (and into) the cytoplasmic membrane.

52
Q

Most translocated proteins contain a signal sequence at the

A

N-terminus that targets the protein to a particular secretion system – often removed after translocation.

53
Q

The Sec secretion system & twin arginine translocase (Tat) are

A

ubiquitous in prokaryotes – others are more specialized

54
Q

The Sec secretion system recognizes a signal sequence in the first ~20
amino acids of protein -

A

translocates unfolded protein before it folds

55
Q

Protein either passed across

A
  • cytoplasmic membrane (SecA pathway)

Or

  • recognized by RNA/protein complex – signal recognition particle - and inserted into membrane (SRP pathway).

Both pathways pass the unfolded protein through a membrane channel - Sec YEG translocon

56
Q

Both pathways for transporting proteins require

A

ATP

57
Q

Tat pathway

A

secretes folded proteins – proteins that

must fold in cytoplasm

Microbiology 200 (32 decks)

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