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MBG 2040 > Week 9 > Flashcards

Week 9 Flashcards

1
Q

What is tRNA?

A

= transfer RNA

- the adapter molecule that forms the interface between amino acids and mRNA in protein synthesis

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2
Q

What is rRNA?

A

= ribosomal RNA

- structural and catalytic components of ribosomes

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3
Q

What is RNA editing?

A

= when information content of genes is changed by

1) changing the structures of individual bases (tRNAs, rRNAS)
2) mRNA is modified by endogenous guide RNAs
3) uridine monophosphate residues are deleted or inserted

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4
Q

When does RNA editing occur?

A

after transcription

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5
Q

What are guide RNAs?

A

= small RNAs that are synthesized in cells

  • can insert U residues into an mRNA
  • mRNA and guide RNA hydrogen bond where they are complementary but unpaired loops also form in guide RNA
  • a repair polymerase can use the unpaired A residues in the guide RNA s a template and insert complementary U residues at these positions
  • permanent modification! = new codons, new amino acids in polypeptide
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6
Q

How can enzymes edit mRNA?

A

= example is cytidine deaminase

  • can convert C residues in mRNA to U residues and alters the mRNA codons
  • example: CAA (glutamine codon) is turned into UAA which generates a premature stop codon and resutls in truncated polypeptide, which will have a different function
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7
Q

Who postulated the existence of tRNA?

A

Francis Crick in 1956 = as adapter b/n amino acids and codons in mRNA

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8
Q

What function do tRNAs serve?

A

= permit codons in mRNA to be read as amino acids by the ribosomes

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9
Q

What is the recognition sequence of tRNA?

A

= the 3’ end of tRNA has a recognition sequence that reads 5’ CCA 3’
- used for covalent joining of the amino acid that corresponds to that particular tRNA

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10
Q

What is the anticodon sequence of tRNA?

A
  • a sequence that corresponds to an mRNA sequence and can undergo complementary base pairing with this corresponding codon in the mRNA
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11
Q

What kinds of nucleotides are contained in tRNA?

A
  • modified ribonucleotides

- created by tRNA modifying enzymes

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12
Q

What are ribosomes composed of?

A
  • a small subunit and a large subunit
  • both are assembled from many different proteins and rRNAs
  • it is an “RNA machine” with key roles in protein synthesis, including formation of peptide bonds between amino acids
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13
Q

How are prokaryotic rRNAs made?

A

= by prokaryotic RNA polymerase

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14
Q

How are eukaryotic rRNAs made?

A

= the larger rRNAs are made by RNA polymerase I and the smaller rRNAs are mad by RNA polymerase III

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15
Q

What is the 16S rRNA in prokaryotes?

A

= helps form the small ribosomal subunit and carries the complementary sequence to the Shine-Delgarno sequence in the mRNA that specifies ribosome assembly

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16
Q

What is the nucleolus?

A

= site of eukaryotic rRNA synthesis and ribosome assembly

a nuclear sub-region (dark staining very chromatin dense but no nuclear enveloppe)

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17
Q

Where does ribosome assembly occur in prokaryotes?

A

= since there is no nucleus, rRNA synthesis and ribosome assembly occur in cytoplasm

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18
Q

How are mature rRNAs formed?

A
  • enzymes modify and trim precursor rRNA transcripts to mature forms in the cell
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19
Q

What is the difference between mature prokaryotic and eukaryotic rRNAs?

A

Prokaryotic: results in mature RNAs: 16S rRNA, 23S rRNA, 5S rRNA as well as tRNA

Eukaryotic: 18S rRNA, 5.8S rRNA, 28S rRNA

result of the long precursor rRNA transcript being processed and ribonucleotide modifications to form mature forms

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20
Q

What are snRNAs?

A

small nuclear RNAs
act as complexes with proteins
play roles in post-transcriptional processing of RNA (like splicing - spliceosome assembly)

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21
Q

What are snoRNAs?

A

small nucleolar RNAs
also act in complexes with proteins
- in eukaryotes: guide the enzymatic chemical modifications of ribosomal RNAs, transfer RNAs, and small nuclear RNAs

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22
Q

What are examples of small micro RNAs?

A
  • siRNA (small inhibitory RNA)
  • miRNA (microRNA)
  • CRISPR RNA
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23
Q

What are common features of small micro RNAs in eukaryotes?

A
  • act as short (22 nucleotides), single-stranded RNAs that bind to complementary sequences
  • produced by cleavage of mRNAs, RNA transposons, and RNA viruses
  • regulate and control gene expression in different ways
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24
Q

What does siRNA do?

A

binds to mRNA and inhibits translation

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25
Q

What does miRNA do?

A

binds to mRNA and causes it to be degraded

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26
Q

What are features of small micro RNAs in prokaryotes?

A
  • CRISPR RNA: encoded by DNA sequences found in prokaryotic genomes
  • works in association with prokaryotic Cas9 nuclease to cleave foreign DNA that might happen to enter a host cell (prevents incorporation of foreign DNA into host genome - a bacterial defense system)
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27
Q

What are long noncoding RNAs?

A

= known to function in eukaryotic cells and are longer than micro-RNAs (200-100000 nt long)
- about 80% of mammalian genome consists of non-protein coding RNAs

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28
Q

What is the function of long non-coding RNAs?

A
  • regulate and control gene expression at the level of transcription/translation by binding mRNA or sequestering micro-RNAs that control gene expression
    OR
  • bind and recruit proteins involved in DNA modification (Xist RNA controls binding of proteins that methylate DNA sequences contributing to X chromosome inactivation in mammals)
29
Q

What causes sickle-cell anemia?

A

= caused by a single amino acid change (Glu to Val) in one of the protein chains that make up hemoglobin in red blood cells

30
Q

Where are DNA sequences found and how does it result in a protein?

A

in the gene, which is then transcribed to make mRNA (in eukaryotes this has to be processed) then finally the mRNA is translated into a protein by the ribosome and accessory proteins

31
Q

Why does mRNA generally last longer in eukaryotes?

A
  • because it is first transcribed in nucleus and then translated in the cytoplasm rather than having a simultaneous process
32
Q

What does one gene result in in terms of protein products?

A

one colinear polypeptide

33
Q

What in a gene specifies a colinear sequence?

A

= the sequence of base pair triplets in the coding region of the gene
= results in the colinear sequence of amino acids in its polypeptide product

34
Q

What did Beadle and Tatum find?

A
  • in 1930ies found that one gene encoded one discrete polypeptide
  • through genetic analysis of nutritional mutants in fungus Neurospora
35
Q

What did Charles Yanofksy and colleagues find?

A
  • in 1960ies they found through mutational/biochemical analysis that the sequence of nucleotide triplets in trpA gene of E coli corresponded to teh sequence of amino acids in trpA protein
36
Q

What do the sequential triplet codons of the gene specify?

A

= the order series of amino acids in protein

37
Q

What are proteins?

A
  • chains of amino acids

- aka polypeptides

38
Q

Describe an amino acids

A

have a free amino group, a free carboxyl group, and a side group (R)

39
Q

How are amino acids joined together?

A

= by peptide bonds

  • carboxyl group of one amino acid is covalently attached to the amino group of the next amino acid
  • happens through elimination of H2O
40
Q

What is the primary structure of a protein?

A
  • the linear arrangement of amino acids
41
Q

What is the secondary structure of a protein?

A

= determined by spatial organization of amino acids (beta sheet, alpha helix)

42
Q

What is the tertiary structure of a protein?

A

= determined by the overall folding of the complete polypeptide in space

43
Q

What is the quaternary structure of a protein?

A

= only in some proteins - when more than one polypeptide interacts to make a functional protein
- multi-subunit proteins

44
Q

Why is the triplet code the only code that makes sense?

A
  • because 4(bases)^3 = 64 possible codons, sufficient for synthesis of 20 amino acids if some of thema re specified by more than one codon (which they are)
  • 4^2 and simply 4 would not give enough for 20 AA
45
Q

How was triplet code confirmed?

A
  • through mutant analysis by Francis Crick and colleagues in 1961
46
Q

Which researchers played critical role in breaking the triplet code?

A

Marshall Nirenberg, Gobind Khorana, Philip Leder

47
Q

What was one way in which the order of ribonucleotides in triplet code was solved?

A
  • by making synthetic homopolymers and adding them to a bacterial cell extract capable of making proteins`
  • produce homopolypeptides
  • could figure out what amino acids some of the codons specified
48
Q

What are homopolymers?

A

= synthetic mRNAs of repeated sequence

49
Q

What does UUU code for?

A

Phe

50
Q

What does AAA code for?

A

Lys

51
Q

What does CCC code for?

A

Pro

52
Q

How were co-polymers used in breaking the triplet code?

A
  • if take an mRNA 5’ UCC UCC UCC 3’ sequence then it produces ser, pro, leu
  • suggests that UCC serine, CCU, pro. and CUC leuc
  • depending on where translational reading frame begins, i.e. where ribosome starts translation
53
Q

What effect do short mRNAs have on ribosomes?

A
  • Nirenberg and Leder demonstrated that short mRNAs of known sequence stimulate the binding of ribosomes and the corresponding amino-acid bound tRNA
  • helped in identifying the amino acids specified by all mixed codons
  • allowed them to show that tRNA and bound amino acids are specific to each codon
54
Q

What does GUU specificy?

A

Valine

55
Q

How many possible triplet are there?

A

64

56
Q

How many triplets specify amino acids?

A

61

57
Q

Are there any triplets that don’t specify AA?

A

yes, 3 triplets specify codons which terminate translation

58
Q

What are the stop codon triplets?

A

UAG, UGA, UAA

59
Q

What is degeneracy in the genetic code?

A

some amino acids have more than one codon in the genetic code

60
Q

Why is the genetic code said to be comma-free?

A

b/c each mRNA has consecutive codons that specify amino acids and there are no breaks or pauses in the mRNA

61
Q

Does the genetic code vary between species?

A

No, nearly all species use the same code, with rare exceptions such as some genes for mitochondrial proteins

62
Q

Where is degeneracy in the genetic code found?

A

at the third codon position

i.e. GCU, GCA, GCG, GCC all specify Alanine

63
Q

What is the reason for degeneracy?

A
  • relaxation of the stringency of base pairing at the third codon (wobble) position (b/n mRNA codon and aminoacyl tRNA)
    ex.:
    3’ AGG 5’ can undergo base pairing with either 5’ UCC 3’ or 5’ UCU 3’ - flexibility is at third codon (both specify Ser)
64
Q

What is the wobble position?

A

the 3rd codon position or the 1st anti-codon position

65
Q

Which AA are only specified by one triplet?

A

tryptophan and methionine

66
Q

What does the Wobble hypothesis explain?

A

= how a single tRNA can respond to two or more codons

67
Q

What is inosine?

A

a modified guanine/adenine derivative, can be found in the 1st anti-codon position in some tRNAs

68
Q

Where does stringent base pairing occur in codon recognition?

A

b/n codon in mRNA and the anti/codon in tRNA only at the first two bases of the codon

69
Q

How many hydrogen bonds are found at the wobble position?

A

there are two bonds between A=I, C=I, U=I and U=G

regular base pairing GC AU only at 1st and 2nd codon positions and 2nd and 3rd anticodon

MBG 2040 (9 decks)

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