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Biology > From DNA to protein: How Cells Read the Genome > Flashcards

From DNA to protein: How Cells Read the Genome Flashcards

1
Q

How does RNA differ from DNA?

A

Sugar Difference: Ribose is used in RNA and deoxyribose is used in DNA

Base Difference: Urail in RNA; Thymine in DNA

Strand: RNA is mostly single stranded; DNA is double stranded

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2
Q

Why might RNA being single strand be significant?

A

It can fold into a variety of shape which allows RNA to carry out multiple functions in cells

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3
Q

How is RNA made in a cell?

A

Through Transcription

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4
Q

Describe the process of transcription

A
  1. A small portion of the DNA double helix is opened. RNA bind to promoter (initiation)
  2. Ribonucleotides are added. The nucleotide sequence is determined by the complementary base pairing with the DNA template strand. (elongation)
  3. RNA polymerase linked ribonucleic triphosphate to the growing RNA chain
  4. RNA polymerase reach stop point and release the RNA chain (termination)
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5
Q

What synthesizes RNA

A

RNA polymerase

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6
Q

What is difference from RNA polymerase to DNA polymerase?

A

RNA polymerase does not need a primer

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7
Q

What does RNA polymerase do to synthesize RNA?

A

Catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the sugar–phosphate
backbone of the RNA chain

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8
Q

What is a promoter?

A

DNA sequence that is recognized by RNA polymerase as a start point

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9
Q

Why is a promoter important?

A

RNA polymerase must recognize the starting point on a gene, thus promoter have DNA sequence that is recognized by RNA polymerase as a starting point

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10
Q

How does a RNA polymerase know when to stop elongation?

A

When it encounters a second signal in the DNA: the terminator

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11
Q

What are the three stages of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
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12
Q

Describe Initiation in transcription

A

RNA polymerase binds to a sequence of DNA called the promoter.

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13
Q

Describe Elongation in transcription

A

The polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5’ to 3’.

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14
Q

Describe Termination in transcription

A

Sequences called terminators signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase.

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15
Q

What can a cell do to make more of a certain protein?

A

They can have transcription amplify expression of genetic material.

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16
Q

Describe the process of transcription in bacterial

A
  1. Initiation
    Sigma factor recognize the promoter sequence and direct binding of RNA polymerase to promoter
  2. Elongation
    RNA polymerase moves forward and continues synthesizing the RNA. Sigma factor is released
  3. Termination
    After transcribing the terminator sequence, the enzyme halts and releases both the DNA template and the newly
    made RNA transcript.

RNA polymerase binds to with a free sigma factor and search for another promoter

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17
Q

Where does the promoter bind to?

A

TATA box

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18
Q

Why is it important that the promoter are asymmetrical?

A

To ensures that RNA polymerase is correctly oriented on the promoter so it can transcribe in only one direction

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19
Q

How does transcription differ in eukaryotes than in prokaryotes?

A
  1. RNA polymerase
  2. Initiation
  3. Transcript Process
  4. Nucleosome packaging
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20
Q

How does transcription differ between eukaryotes and prokaryotes in rna polymerase?

A

Prokaryotes only have one type of RNA polymerase while Eukaryotes have three types.

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21
Q

How does transcription differ between eukaryotes and prokaryotes in initiation?

A

Prokaryotes RNA polymerase can initiate without helper protein while Eukaryotes RNA polymerase require a transcription factor.

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22
Q

How does transcription differ between eukaryotes and prokaryotes in transcript process?

A

Eukaryotic RNA must be process while prokaryotes are generally not process.

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23
Q

How does transcription differ between eukaryotes and prokaryotes in nucleosome packaging?

A

Eukaryotes have nucleosome while prokaryotes don’t.

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24
Q

What are the roles of general transcription factors in eukaryotic cells?

A

TATA Binding Protein (TBP)
- Binds to TATA box

TFIID: Enables the binding of TFIIB

TFIIB and other transcription factor: assemble promoter

Help bind the

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25
Q

What are the roles of general transcription factors in eukaryotic cells?

A

TFIID: Binds to the TATA box

TBP: Subunit of TFIID that binds the whole transcription factor to the TATA box

TFIIB (and other TF): assemble promoter

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26
Q

Describe the transcript initiation of RNA polymerase II

A
  1. TFIID binds to the TATA box
  2. Assembly of transcription initiation complex on promoter
    ( TFIIB + RNA polymerase + TFIIF + other)
  3. TFIIH phosphorylate RNA polymerase II’s tail
  4. General transcription factors release from DNA once
    transcription begins
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27
Q

Why does RNA processing occur in eukaryotic cells?

A

To remove irrelevant RNA codes and make the RNA Ready for reading/recognition.

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28
Q

Where does transcription take place?

A

Nucleus

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29
Q

What are the three steps of RNA processing?

A
  1. RNA capping
  2. Polyadenylation
  3. Splicing
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30
Q

How does RNA capping work?

A

attaching a guanine (G) nucleotide bearing a methyl group to the 5’ end of the RNA

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31
Q

How does polyadenylation work?

A

An enzyme adds a series of repeated adenine (A) nucleotides to the trimmed end to 3’ end of the RNA

32
Q

How does RNA capping and polyadenylation affect RNA?

A

1.Increasing the stability of mRNA
2. Facilitate mRNA transport from the nucleus to cytosol
3. Mark an RNA as mRNA
4. Used by protein synthesis machinery as indicators that the mRNA sequence is complete

33
Q

What are introns?

A

Noncoding, intervening sequences that can interrupt a stretch of coding sequence

34
Q

What are exons?

A

Pieces of coding sequence

35
Q

What happens during RNA splicing?

A

The introns are removed from the newly synthesized RNA
and the exons are stitched together

36
Q

What must happen before an RNA can leave the nucleus to become a protein?

A

RNA splicing must occur to remove all introns

37
Q

What removes the introns?

A

Spliceosome

38
Q

What are Spliceosome?

A

Large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus.

39
Q

What is spliceosome good for?

A

Create diversity in the types of proteins that a single line of RNA

40
Q

What is functional diversity in RNA good for?

A

Different part of the bodies may require this particular RNA. Therefore, alternative splicing can splice RNA in a way that suits the body’s need

41
Q

What makes an RNA mature?

A

No introns, broken strands or incorrectly spliced variants.

42
Q

What takes the mature RNA out of the nucleus and into the cytosol?

A

Transport protein

43
Q

How does transport protein know if an RNA can exit the nucleus?

A

Poly a tail and methyl cap

44
Q

How does transcription differ in prokaryotes and eukaryotes?

A

Eukaryotes have to process (capping, splicing ) their RNA

45
Q

What happens if transcription were to stop?

A

Cell dies

46
Q

What is the START codon (MET)

A

AUG

47
Q

What is the STOP codon

A

UAA, UAG, UGA

48
Q

Why is the site of transition initiation crucial?

A

The same mRNA sequence can specify three completely
different amino acid sequences, depending on the nucleotide at which translation begins which may produce a different protein

49
Q

What are tRNA?

A

Adapter molecules that link codons with amino acids

50
Q

What is a wobble position in tRNA?

A

Third nucleotide in a codon that and it is the redundancy in the genetic code such that the same amino acid may be encoded by multiple codons.

51
Q

What is aminoacyl-tRNA synthetase

A

Enzyme that attaches the appropriate amino acid onto its corresponding tRNA.

52
Q

What are ribosomes?

A

Complex that synthesizes protein

53
Q

What are ribosomes made out?

A

small protein (ribosomal protein) and RNA (rRNA)

54
Q

What does the large subunit of the ribosome do?

A

catalyzes formation of peptide bonds

55
Q

What does the smaller subunit of the ribosome do?

A

matches tRNAs with codons

56
Q

What are the three binding sites for tRNA?

A

A site, P site, E site

57
Q

What is the A site of a ribosome?

A

aminoacyl-tRNA: charged tRNA binds to its mRNA codon

58
Q

What is the P site of a ribosome?

A

peptidyl-tRNA: condensation of amino acids

59
Q

What is the E site of a ribosome?

A

exit: where the “uncharged” tRNA is ejected

60
Q

How does translation begin

A
  1. tRNA charged with MET binds to the P site with the help of translation initiation
  2. Once bound to the P site, the initiator factor dissociate and large ribosomal subunit binds and assemble
  3. tRNA are added
61
Q

How does translation initiation work in prokaryotes?

A

Prokaryotic ribosomes initiate translation
at ribosome-binding sites. Different proteins can be synthesized simultaneously with each protein at a different ribosome

62
Q

Describe the process of translation elongation

A
  1. Newly bound charged tRNA bind at A site
  2. Peptide bond connect to the RNA at the A site
  3. Large subunit translocate
  4. Smaller subunit translocate, ejecting the tRNA that was moved from P site to E site
63
Q

What are polyribosomes

A

Multiple ribosomes initiate on a single mRNA

64
Q

What is the significant of polyribosomes?

A

Many more protein molecules can be made
in a given time

65
Q

What can happen to a protein after translation for the protein to become fully functional?

A
  1. Folding
  2. Phosphorylation
  3. Glycosylation
  4. Association with Subunits
66
Q

What are proteolysis?

A

Enzymes that degrade protein

67
Q

How does proteolysis degrade protein?

A
  1. By cutting (hydrolyzing) the peptide bonds between amino acid
68
Q

Why is proteolysis important?

A

They can recognize and remove proteins that are damaged or misfolded

69
Q

Why is it important that misfolded or damaged protein be removed?

A

Misfolded proteins tend to aggregate, and protein aggregates can damage cells and even trigger cell death

70
Q

How do proteasomes select which proteins in the cell should be degraded?

A

They act on protein that are marked by a protein called ubiquitin

71
Q

What does ubiquitin do?

A

Mark proteins for proteasome to degrade

72
Q

Describe the process on how proteasome degrade protein

A

Proteasome forms a cylinder in which proteins are bound inside and degraded, releasing amino acids.

73
Q

In terms of processing, what is different about eukaryotic RNA than prokaryotic RNA

A

In eukaryotes, nearly all steps of making a protein can be regulated

74
Q

What can antibiotic be used for?

A

Inhibiting bacterial ribosomes but not eukaryotic
ribosomes

75
Q

What are RNAi

A

RNA that protects cells from infections and block synthesis of foreign RNA

76
Q

Describe the process of how RNAi protect cells from infections

A
  1. RNAi detects foreign RNA (dsRNA)
  2. Foreign RNAs are cut into short
    fragments (siRNA) by dicer

3.Foreign ssRNA loaded to the RNA
induced silencing complex (RISC)

  1. RISC targets other foreign RNAs for
    its degradation
77
Q

Describe the process of RNAi blocking synthesis of foreign RNA

A
  1. Detection of foreign dsRNA
  2. Foreign RNAs are cut into short
    fragments (siRNA) by dicer
  3. Foreign ssRNA loaded to the RNA
    induced transcriptional silencing (RITS)
  4. RITS complex attaches to newly
    synthesized RNA, attracts heterochromatin
    creating proteins to halt transcription

Biology (20 decks)

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