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Protein: Structure, Genetic Code & Synthesis Flashcards

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1
Q

(T/F) To get from DNA to protein, the decoding of mRNAs by tRNAs has to take place.

A

True!

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2
Q

What are the three RNAs involved in protein synthesis?

A

1) mRNA
2) tRNA (forms complex structures that allows mature mRNA and ribosome to communicate)
3) rRNA

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3
Q

Match the following RNAs to their definition:

1) mRNA
2) tRNA
3) rRNA

A) contains a specific three-nucleotide anticodon sequence that each amino acid type is covalently bound to. The anti-codon base pairs with its complementary mRNA codon to position the encode aa in the ribosome A site where it is covalently linked to the C-terminus of the growing peptide.

B) a form catalyzes peptide bond formation between incoming aa-tRNA amino group and the carboxy-terminus of the growing protein chain

C) nucleotide sequence encodes the order of amino acids that a ribosome assembles into a polypeptide chain

A

mRNA: nucleotide sequence encodes the order of amino acids that a ribosome assembles into a polypeptide chain

tRNA: contains a specific three-nucleotide anticodon sequence that each amino acid type is covalently bound to. The anti-codon base pairs with its complementary mRNA codon to position the encode aa in the ribosome A site where it is covalently linked to the C-terminus of the growing peptide.

rRNA: a form catalyzes peptide bond formation between incoming aa-tRNA amino group and the carboxy-terminus of the growing protein chain

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4
Q

What is a ribozyme?

A

A nucleic acid (rRNA) that acts as an enzyme by facilitating bond formation between incoming aa-tRNA amino group and the carboxy-terminus of the growing protein chain

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5
Q

What is a major evidence that shows that RNA came before proteins?

A

Ribozymes!!!

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6
Q

Fill in the blank:

Each amino acid is encoded by a _____ nucleotide codon, which is the shortest possible code for _____ bases to encode _____ amino acids.

A

Three; four; 20

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7
Q

Even tho 4^3 results in 64 possible codons to encode for 20 amino acids, why do only 61 codons encode 1 of the 20 amino acids?

A

There are three stop codons! UAA, UGA, and UAG!

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8
Q

While most amino acids are encoded by more than one codon (degenerate code), which amino acids are encoded only by a single codon?

A

Methionine

Tryptophan

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9
Q

(T/F) Code is not overlapping. Translation of prokaryotic and eukaryotic cell polypeptide chains begins with AUG start codon encoding methionine.

A

True!

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10
Q

What safeguards against missense mutation?

A

Missense mutation: change in amino acid

REDUNDACY (property of ribosome) and WOBBLE-PAIRING safeguards against missense mutations.

Wobble pairing leads to silent mutation -> same amino acid encoded!

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11
Q

How many reading frames in a mRNA sequence?

Which one is the correct frame for most proteins?

A

Non-overlapping triplet genetic code without divisions between codons can be translated in THREE DIFFERENT READING FRAMES (aka open reading frames)!

The frame initiated by the most 5’ AUG start codon and the one that is not riddled with STOP codons until the very end is the correct frame for most proteins.

Other two have a very high chance of having lots of STOP codons early on in the sequence.

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12
Q

What can change the polypeptide sequence (reading frame)?

A

FRAME SHIFTING caused by base addition or deletion!

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13
Q

What synthesizes pre-tRNAs and what must they undergo to become mature tRNAs?

A

RNA polymerase III synthesizes pre-tRNAs and they must undergo EXTENSIVE CLEAVAGE and BASE MODIFICATION in the nucleus to become mature!

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14
Q

What is cleaved in the pre-tRNAs to become mature tRNAs and by what?

A

1) 14-nucleotide intron in the anticoding loop, removed by splicing
2) 16-nucleotide 5’ end sequence, cleaved by RNase P

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15
Q

How are tRNA bases modified? How many of the bases are modified?

A

1) 3’ end U residues replaced with a CCA sequence
2) Specific uridines converted to dihydrouridine, pseudouridine or ribothymidine residues

10% of the bases are modified!

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16
Q

Why are the 3’ end U residues replaced with a CCA sequence?

A

CCA sequence is required for tRNA charging with amino acid by AMINOACYL-tRNA SYNTHETASE.

*enzyme connects amino acid to the tRNA with the anti-codon specific for that aa.

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17
Q

How does the AMINOACYL-tRNA SYNTHETASE function as a tRNA quality control point?

A

Only properly folded tRNAs recognized by it!

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18
Q

What do the base modifications of the tRNA molecule result in?

A

1) Stabilization of the tRNA molecule
2) Stabilization during ribosomal interactions

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19
Q

Fill in the blanks:
The ___-shaped folded structure of the tRNA (__-__ nucleotides long), with the anticodon and amino acid acceptor stem on the ends of the two arms, promotes its _______ functions.

A

L-shaped; 70-80 nucleotides long; DECODING

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20
Q

What is the first step of Aminoacyl-tRNA synthetase coupling amino acid to tRNA?

A

An aminoacyl-tRNA synthetase couples a specific amino acid via a high-energy ester bond (making the amino acid activated) to either the 2ʹ or 3ʹ hydroxyl of the terminal adenosine in the tRNA
that has the proper anticodon (cognate tRNA).

So basically, get a mature tRNA and give it the right amino acid!

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21
Q

What does the energy of the high ester bond in the first step of Aminoacyl-tRNA synthetase coupling amino acid to tRNA drive the formation of?

A

The energy of the ester bond subsequently drives the formation of the PEPTIDE BONDS linking adjacent amino acids in a growing polypeptide chain in the ribosome!

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22
Q

What is the second step of Aminoacyl-tRNA synthetase coupling amino acid to tRNA?

A

The anticodon three-base sequence in the tRNA base-pairs with a
complementary codon in the mRNA specifying the attached amino acid.

In simpler words, tRNA with the right aa goes and bonds to mRNA!

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23
Q

How are the anticodon three nucleotides located to be accessible for codon-anticodon base pairing?

A

In a LOOP!

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24
Q

What are the four characteristics shared by all tRNA structures?

A

1) Fold into four base-paired stems and four loops

2) Have a CCA sequence at the 3’ end (acceptor stem) to which an amino acid is attached by aminoacyl tRNA synthetase

3) Have a anticodon triplet at the tip of the anticodon loop

4) Have post-transcriptionally modified A, C, G, and U residues

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25
Q

Which directions are the anticodons? Which direction is the mRNA?

A

Anticodons 3’ -> 5’

mRNA 5’ -> 3’

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26
Q

(T/F) Nonstandard base pairing of base in the anticodon wobble position (first position of anticodon, 5’ base) enables certain tRNAs to base-pair with more than one codon (third position of codon, 3’ base) for the same amino acid.

A

True!

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27
Q

Match the following:

1) Inosine in the wobble position of the tRNA
2) G or U in the wobble position of the tRNA
3) A in the wobble position of the tRNA

A) can pair with three different but synonymous codons (C, A, U) in the mRNA codon bearing the same amino acid

B) can pair with two codons

C) is rare in nature

A

Inosine in the wobble position of the tRNA can pair with three different but synonymous codons (C, A, U in mRNA codon third base position) bearing the same amino acid

G or U in the wobble position of the tRNA can pair with two codons

A in the wobble position of the tRNA is rare in nature

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28
Q

(T/F) Ribosomes differ in bacteria, archaea, and eukaryotes, but share structural and functional similarities.

A

True!

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29
Q

What is the small (30S) subunit of the bacterial ribosome composed?

A

16s rRNA and proteins

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30
Q

What is the large (50S) subunit of the bacterial ribosome composed?

A

23S, 5S rRNAs and proteins

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31
Q

What is the E, P, and A site of the ribosome? In which site does the elongating peptide attach to the tRNA?

A

E - Exit site
P - Peptidyl site
A - Aminoacyl site

Elongating peptide attaches to the tRNA in the P site.

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32
Q

Why do different organisms have different lengths of pre-rRNA transcription units?

A

Variation in the lengths of the transcribed space regions (transcriber space) - the region between the genes.

The coding sequences for the different rRNAs is similar throughout different organisms!

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33
Q

Briefly describe how rRNAs are processed (pre rRNA -> mature rRNA).

A

Nascent pre-rRNA transcripts (synthesized by RNA pol1) is bound immediately by proteins into pre-ribosomal ribonucleoprotein particles (pre-rRNPs).

This is cut in a series of cleavage and exonucleolytic steps to generate the mature rRNAs found in ribosomes.

34
Q

What are endoribonucleases? What are exoribonucleases?

A

Endoribonucleases: internally cleave pre-rRNA transcripts (scissors)

Exoribonucleases: digest from either 5’ and 3’ end (pac-men)

35
Q

(T/F) There are many different RNAs in ribosomes. These are encoded very closely to each other in the genome and are transcribed as a single transcript that is cleaved into different rRNAs.

A

True!

36
Q

How does the eukaryotic ribosomal subunit assemble?

A

rRNA is transcribed in the nucleus, and proteins associate with it during transcription, creating a pre-90S subunit, which is cleaved into pre-40S (small) subunit and pre-60S (large) subunit.

The pre-40S subunit requires only a few more remodelling steps before transport to the cytoplasm to become 40s.

The pre-60S subunit requires considerable modelling through many transient interactions with nonribosomal proteins before export to the cytoplasm to become 60S.

37
Q

The pre-60S subunit of the ribosome has to go through considerable modelling before being transported to the cytoplasm. What are the two main enzymes that are involved? What are their functions?

A

GTPases - involved in quality control checkpoints

ATPases - large molecular movements required to fold the large + complex rRNA into the proper conformation (important for exportation)

38
Q

How are the ribosomal components further matured in the cytoplasm?

A

Removal of export factors

39
Q

RNA constitutes about ___% of the mass of bacterial ribosome and about ___% of the mass of a human ribosome.

A

60; 50

Ribosome is made of proteins and RNA!

40
Q

(T/F) Many antibiotics exploit ribosome differences and inhibit bacterial protein synthesis without affecting the function of mammalian ribosomes.

A

True!

41
Q

How many steps initiate translation in eukaryotes? What do they involve?

A

8!

Eukaryotic translation initiation factors (eIFs) and GTP hydrolysis which stabilizes some complexes

42
Q

Match the following steps of initiation of translation in eukaryotes:

1) Step 1
2) Step 2
3) Step 3
4) Step 4
5) Step 5
6) Step 6
7) Step 7
8) Step 8

A) The 43S preinitiation complex binds an elF4-mRNA complex.

B) Initiation codon recognition causes eIF5 to stimulate HYDROLYSIS of eIF2-bound GTP (2-GTP to 2-GDP), which switches the conformation of the scanning complex to a 48S initiation complex with the tRNAiMet anticodon base-paired to the initiator AUG in
the P site.

C) eIF2-GTP binds to a tRNAi(met) to form eIF2 ternary complex

D) Association of the 40S and 60S subunits causes eIF5B-GTP hydrolysis, release of eIF5B-GDP and eIF1A, forming the 80S initiation complex with tRNAi Met base-paired to the initiation codon in the ribosomal P site.

E) elF2 ternary complex and eIF5 bind RIBOSOME 40S SUBUNIT, which is already bound by eIF1, eIF1A, and eIF3 to form 43S PREINITIATION COMPLEX

F) The 60S subunit joins the 40S subunit, causing binding of eIF5B-GTP to eIF1A in the ribosomal A site and release of most of the earlier-acting eIFs.

G) Multisubunit eIF4 complex binds to mRNA; subunit eIF4E binds to the mRNA 5ʹ cap, and subunit eIF4G binds multiple copies of cytoplasmic poly(A)-binding protein (PABPC) bound to the mRNA poly(A) tail. This circularizes mRNA by forming a bridge between the 5ʹ (cap) and 3ʹ (poly(A)) ends of the mRNA. In parallel to step 1 & 3!

H) eIF4B-stimulated eIF4A RNA HELICASE activity unwinds any RNA secondary structure (hairpins, loops, etc) at the 5ʹ end of the mRNA as the 40S subunit scans in the 5ʹ→ 3ʹ direction until it recognizes the AUG initiation codon (in a conserved Kozak sequence).

A

Step 1: eIF2-GTP binds to a tRNAi(met) to form eIF2 ternary complex

Step 2: elF2 ternary complex and eIF5 bind RIBOSOME 40S SUBUNIT, which is already bound by eIF1, eIF1A, and eIF3 to form 43S PREINITIATION COMPLEX

Step 3: Multisubunit eIF4 complex binds to mRNA; subunit eIF4E binds to the mRNA 5ʹ cap, and subunit eIF4G binds multiple copies of cytoplasmic poly(A)-binding protein (PABPC) bound to the mRNA poly(A) tail. This circularizes mRNA by forming a bridge between the 5ʹ (cap) and 3ʹ (poly(A)) ends of the mRNA. In parallel to step 1 & 3!

Step 4: The 43S preinitiation complex binds an elF4-mRNA complex.

Step 5: eIF4B-stimulated eIF4A RNA HELICASE activity unwinds any RNA secondary structure (hairpins, loops, etc) at the 5ʹ end of the mRNA as the 40S subunit scans in the 5ʹ→ 3ʹ direction until it recognizes the AUG initiation codon (in a conserved Kozak sequence).

Step 6: Initiation codon recognition causes eIF5 to stimulate HYDROLYSIS of eIF2-bound GTP (2-GTP to 2-GDP), which switches the conformation of the scanning complex to a 48S initiation complex with the tRNAiMet anticodon base-paired to the initiator AUG in
the P site.

Step 7: The 60S subunit joins the 40S subunit, causing binding of eIF5B-GTP to eIF1A in the ribosomal A site and release of most of the earlier-acting eIFs.

Step 8: Association of the 40S and 60S subunits causes eIF5B-GTP hydrolysis, release of eIF5B-GDP and eIF1A, forming the 80S initiation complex with tRNAi Met base-paired to the initiation codon in the ribosomal P site.

43
Q

(T/F) The first methionine that binds to the eukaryotic initiator factor 2 is a little different from the other METs, to indicate the start MET.

A

True!

44
Q

What is the Kozak sequence?

A

Highly conserved sequence that the ribosome detects for a start codon!

GCCRCCAUGG

Position -3 (R = purine) and +4 (Last G) have a strong effect on TRANSLATION EFFICIENCY!

45
Q

(T/F) Only 1/4th of translation starts from the KOZAK sequence.

A

False! 99% of translation starts from the KOZAK sequence.

46
Q

Break down step 6 of initiation of translation in eukaryotes :

A

1) Initiation codon is recognized
2) Hydrolysis of elF2-GTP by EIF5
3) Scanning complex switched into an initiation phase
4) AUG interacts with tRNAi(met) in the P site

47
Q

Break down step 7 of initiation of translation in eukaryotes :

A

1) 60S interacts with 40S subunit
2) Release of most EIFs, which will re- associate with 5’cap and polyA binding protein complex to initiate synthesis by another ribosome!

48
Q

What are the key steps in chain elongation in eukaryotes?

A

1) ENTRY of each succeeding aminoacyl-tRNA with an anticodon complementary to the next codon into the A site

2) Formation of a peptide bond
catalyzed by large rRNA (ribozymes)

3) TRANSLOCATION of the ribosome one codon at a time along the mRNA.

49
Q

(T/F) During chain elongation, each incoming tRNA moves through three sites: A, P, and E.

A

True!

50
Q

What does chain elongation start with?

A

80S ribosome with Met-tRNAi(Met) in the ribosome P site!

51
Q

Match the following steps of chain elongation in eukaryotes:

1) Step 1
2) Step 2
3) Step 3
4) Step 4

A) EF(elongation factor)1α·GTP hydrolysis causes EF1α conformational change, releasing the EF1α·GDP and positioning the aminoacylated 3ʹ end of the tRNA in the A site close to the 3ʹ end of the Met-tRNAi(Met) in the P site.

B) The large rRNA catalyzes PEPTIDE BOND FORMATION (peptidyl transferase reaction) between Meti and amino acid 2.

C) EF2·GTP hydrolysis causes ribosome conformational change that translocates the ribosome one codon along the mRNA and shifts the unacylated tRNAi(Met) to the E site and the tRNA with the bound peptide to the P site.

D) tRNA-aa2 ternary complex binds to the A site by mRNA codon-tRNA anticodon base pairing.

A

Step 1: tRNA-aa2 ternary complex binds to the A site by mRNA codon-tRNA anticodon base pairing.

Step 2: EF(elongation factor)1α·GTP hydrolysis causes EF1α conformational change, releasing the EF1α·GDP and positioning the aminoacylated 3ʹ end of the tRNA in the A site close to the 3ʹ end of the Met-tRNAi(Met) in the P site.

Step 3: The large rRNA catalyzes PEPTIDE BOND FORMATION (peptidyl transferase reaction) between Meti and amino acid 2.

Step 4: EF2·GTP hydrolysis causes ribosome conformational change that
translocates the ribosome one codon along the mRNA and shifts the unacylated tRNAi(Met) to the E site and the tRNA with the bound peptide
to the P site.

52
Q

What drives the reactions (chain elongation) in one direction?

A

Energy released by GTP hydrolysis at several steps!

53
Q

(T/F) In the second and subsequent elongation cycles, conformational change induced by hydrolysis of GTP
in EF1α·GTP (step 2 of elongation) ejects the tRNA in the E site.

A

True!

54
Q

How many amino acids do ribosomes add per second?

A

three to five amino acids

55
Q

How is translation terminated?

A

Translation is terminated by release factors when a stop codon (UAA, UGA, UAG) is in the A site.

56
Q

What does eRF(release factor)·3GTP hydrolysis cause?

A

eRF3·GTP hydrolysis causes cleavage of the peptide chain from the tRNA in the P site and ejection of the tRNA in the
E site, forming a POST-TERMINATION COMPLEX!

57
Q

During termination of translation, Ribosomal subunits are separated by the action of the ______ ______ together with eIF1, eIF1A, and eIF3 binding
to the __S subunit.

A

ABCE1; ATPase

40

58
Q

What is a polysome?

A

A structure with multiple individual ribosomes simultaneously translating a eukaryotic mRNA.

59
Q

What increases the efficiency of translation?

A

Circular mRNA
Polysomes
Rapid RIBOSOME RECYCLING

60
Q

What determines protein chemical and structural properties?

A

Differences in:
1) Size
2) Shape
3) Charge
4) Hydrophobicity
5) Reactivity
Of the 20 common amino acid side chains

61
Q

What are nine essential amino acids that must be consumed in diet?

A

Isoleucine, Leucine, Tryptophan, Valine, Methionine, Phenylalanine, Threonine, Lysine, Histidine

I Love Tina Very Much Perhaps Tina Loves Harry!

62
Q

What are the most rare amino acids?

A

Cysteine, tryptophan and methionine

*constitute apprs 5% of the aa in a typical protein

63
Q

What are the most common amino acids?

A

Glutamic acid, leucine, lysine, and serine

*constitute apprx 32% of the aa in a typical protein

64
Q

(T/F) Amino acids in proteins can be modified.

A

True!

65
Q

All amino acids consist of a central alpha carbon atom, bonded to four different chemical groups:

A

1) amino (-NH2) group
2) carboxyl or carboxylic acid (-COOH) group
3) Hydrogen atom
4) A side chain (R group)

66
Q

The side chain determines the characteristic properties of each amino acid and is the basis for grouping
the 20 common acids into three main categories:

A

1) Hydrophobic
2) Hydrophilic
3) Special

67
Q

Hydrophobic amino acids have a ______ R group, while hydrophilic amino acids have a _______ R group.

A

Non polar; polar (or ionic groups charged at pH 7)

68
Q

What are the three special amino acids? Why are they special?

A

Cysteine: has reactive sulfhydryl group that can form disulfide bonds

Glycine: single H as a R group, can fit into small spaces in proteins (TRANSMEMBRANE proteins)

Proline: cyclized R group that forms rigid kinks in proteins (limits folding)

69
Q

What are ALIPHATIC amino acids?

A

Alanine, Valine, Leucine + Isoleucine

Linear or Branched HYDROCARBONS that do not form a ring!

70
Q

Why does Methionine differ from the other non-polar aliphatic amino acids?

A

Contains one sulfur atom (still is non-polar)

71
Q

Which amino acids have large, hydrophobic, aromatic rings in their side chains?

A

Phenylalaline, tyrosine and tryptophan

72
Q

What happens to hydrophobic side chains under the influence of HYDROPHOBIC EFFECT?

A

They often pack into the interior of proteins or line the surfaces of proteins in hydrophobic regions of membranes!

73
Q

What makes a hydrophilic amino acid very hydrophilic?

A

Having a side chain that are charged (ionized) at the pH of biological fluids (7) both inside and outside the cell.

74
Q

Which amino acids have a positively charged side chains and therefore referred as BASIC amino acids?

A

Arginine, lysine, histidine

75
Q

Which amino acids have a negatively charged side chains and therefore referred as ACIDIC amino acids?

A

Aspartic acid and glutamic acid

76
Q

What are the polar amino acids without a charged R group?

A

Asparagine, glutamine, serine and threonine

77
Q

(T/F) Thiolate anions (S-) in certain enzymes can play important roles in catalysis, notably in some proteases that destroy proteins.

A

True!

The side chain of cysteine contains a reactive sulfhydryl group (-SH). On release of a proton, a sulfhydryl group is converted into a thiolate anion (S-)!

78
Q

What are the two functions of disulfide bonds?

A

1) CROSS-LINK REGIONS -intra/intermolecular cross linking of peptides
2) STABILIZE the folded structure of some proteins

79
Q

In which proteins are disulfide bonds most common?

A

In proteins that are secreted from cells or that extend outward from the plasma membrane into the extracellular fluid!

80
Q

How is a covalent disulfied bond formed?

A

Two adjacent sulfhydryl groups, like the one in cysteine, can be oxidized and each releases a proton and an electron.

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