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Biochemistry > Chapter 7- RNA and The Genetic Code > Flashcards

Chapter 7- RNA and The Genetic Code Flashcards

1
Q

MRNA is synthesized in what direction?

A

5 to 3 and N to C

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2
Q

mRNA

A

Carries the information specifying the amino acid sequence of a protein to the ribosome.

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3
Q

MRNA in prokaryotes vs eukaryotes protein products

A

mRNA in prokaryotes are polycystronic meaning that one mRNA can result in different proteins.

In eukaryotes mRNA is monocystronic meaning that one mRNA only translates into one protein product.

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4
Q

tRNA

A

Responsible for converting the language of nucleic acids to the language of amino acids and peptides.

Includes a three nucleotide anti-codon. While inside the ribosome the tRNA anti-codon pairs with an appropriate codon and an mRNA molecule.

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5
Q

How many amino acids are in the eukaryotic proteins

A

20

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6
Q

Where in the cell is the tRNA found?

A

In the cytoplasm

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7
Q

What enzyme transfers activated amino acids to the end of the correct tRNA?

A

aminoacyl-tRNA synthetase

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8
Q

What end of the tRNA does aminoacyl tRNA synthetase transfer activated amino acids?

A

3’ end

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9
Q

rRNA

A

RNA helps catalyzes the formation of peptide bonds and is also important and spicing out its own entrance within the nucleus

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10
Q

What is the code on that is considered the start codon?

A

Methionine AUG

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11
Q

What are the three stop codons?

A

UAA UGA UAG

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12
Q

Which two amino acids are only coded for one codon?

A

Methionine and tryptophan

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13
Q

A mutation that only affects one of the nucleotides in a codon

A

Point mutation

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14
Q

Expressed mutation

A

When a point mutation affects the primary amino acid sequence of a protein

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15
Q

What are the two types of expressed mutations?

A

Missense mutation- A mutation where the error codes for another amino acid

Nonsense mutation- A mutation where the codon now in codes for a premature stop codon also known as a truncation mutation.

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16
Q

Frameshift mutation

A

When a nucleotide is added or deleted from the mRNA sequence

A mutation that causes a shift in the reading frame that usually results in changes in the amino acid sequence or premature truncation of the protein

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17
Q

DNA cannot leave the nucleus what does it do to overcome this?

A

DNA must use RNA to transmit genetic information.

MRNA is the only type of RNA that carries information from DNA directly.

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18
Q

Transcription results and what type of mRNA?

A

Single stranded

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19
Q

Template strand AKA

A

Antisense

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20
Q

Which DNA dependent RNA polymerase binds to the promoter region

A

RNA polymerase II

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21
Q

What is the name of the promoter region that RNA polymerase to bind to in eukaryotes?

A

TATA box

Named for its high concentration of thiamine and adenine bases.

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22
Q

Does RNA polymerase require a primer to bind?

A

No, unlike DNA polymerase three in DNA replication RNA polymerase two does not require a primer to start generating a transcript.

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23
Q

Where are the following RNA polymerase is located and what do they synthesize?

RNA polymerase I-

RNA polymerase II-

RNA polymerase III-



A

RNA polymerase I- located in the nucleus synthesizes rRNA

RNA polymerase II- located in the nucleus synthesizes hnRNA

RNA polymerase III- located in the nucleus synthesizes tRNA and some rRNA

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24
Q

Does RNA polymerase proofread?

A

No

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25
Q

What is the difference between the coding strand (sense) and the template strand?

A

Thymine nucleotides in turc coding/sense/template strand are replaced with Uracil nucleotides in the mRNA molecule.

26
Q

Coding strand

A

AKA sense, template strand

27
Q

Upstream versus downstream directions

A

Upstream
To the left
Toward the five prime end
Negative numbers

Downstream
To the right.
Towards the three prime end.
Positive numbers

28
Q

Where does the Tata box normally fall

A

Around -25

29
Q

Transcription continues until

A

It reaches either a termination sequence or stop signal.

30
Q

What is the first result of transcription before it is converted into mRNA?

A

hnRNA after posttranscriptional modifications

31
Q

What three processes transform hnRNA into mRNA?

A

1) Exons spliced out by splicesome
2) 5’ cap (7 methylguanate triphosphate) cap
3) Polyadenosyl tail added to 3’ end (time bomb)

32
Q

Alternative splicing

A

Splicing together the hnRNA in different ways to produce multiple variants of proteins encoded by the same original gene. This allows for the genetic production of many more proteins from a limited number of genes.

33
Q

How does mRNA exit the nucleus?

A

Through nuclear pores

34
Q

When RNA is translated into proteins what direction is the mRNA read?

A

5’ to 3’

35
Q

What are the three binding sites in the ribosome for a tRNA?

A

A site- aminoacyl
P site- peptidyl
E site- exit

36
Q

The composition of prokaryotic versus eukaryotic ribosomes

A

Eukaryotic 40+60 = 80 S subunit.

Prokaryotic 30+50 = 70 S subunit.

37
Q

Where does translation occur?

A

In the cytoplasm of the cell

38
Q

What are the three stages of translation?

A

Initiation, elongation, termination.

39
Q

What are the steps of initiation?

A
  1. The small ribosomal subunit binds to the mRNA in the 5’ untranslated region at the start codon methionine in the p site of the ribosome.

The large subunit and binds to the small subunit forming a complex.

40
Q

The small subunits in the initiation phase binds to what specifically in prokaryotes versus eukaryotes?

A

Prokaryotes: Shine-Delgarno Sequence

Eukaryotes: 5’cap structure

41
Q

What is the initial amino acid in prokaryotes versus eukaryotes

A

Eukaryotes: methionine

Prokaryotes: N-formylmethionine (fMet)

42
Q

What are the steps of elongation?

A

Three step cycle that is repeated for each amino acid that is added to the protein after methionine.

Ribosomes move along the mRNA in the five prime to three prime direction synthesizing the Protien from N. to C terminus.

A- The a site holds the incoming amino acid that is being added to the growing chain.

P-The p site holds the tRNA that carries the growing polypeptide chain. It is also where the first amino acid methionine binds. Requires GTP to form peptide bonds.

E-The e site is where now inactivated or uncharged tRNA pauses before exiting the ribosome. It quickly unbinds from the mRNA and is ready to be recharged.

43
Q

What enzyme uses GTP to form peptide bonds? What part of translation does this occur?

A

Peptidyl transferase

Elongation at the P site

44
Q

Elongation Factors

A

Assist in recruiting aminoacyl tRNA and GTP for translation. Helps remove GDP once the energy has been used.

45
Q

What are the steps of termination?

A

When any of the three stop codons move into the A site, a protein called release factor (RF) binds to the termination codon.

A water molecule is added to the polypeptide chain. This allows peptidyl transferase and termination factors to hydrolyze (cut) the completed polypeptide chain from the final tRNA.

The polypeptide chain is then released from the tRNA in the P site and the two ribosomal subunits dissociate.

46
Q

What processes are included in post translational modifications?

A

1) Chaperones assist in the proper folding of proteins
2) Cleavage
3) Adding other biomolecules to the peptide via:

Phosphorylation (adding phosphate)
Carboxylation (adding carboxylic acid)
Glycosylation (adding oligosaccharides)
Prenylation (adding lipids)

47
Q

Operon

A

Controls gene expression in prokaryotic cells.

Cluster of genes transcribed as a single mRNA.

Divided into operator, promoter and gene regulator.

48
Q

Operator site

A

Upstream of the gene of interest (structural gene) non transcribable region of DNA capable of binding a repressor protein.

49
Q

Promoter Site

A

Further upstream from gene of interest.

Provides a place RNA polymerase to bind.

50
Q

Regulator gene

A

Furthest upstream.

Codes for protein known as the repressor.

51
Q

What are the two types of operons?

A

Inducible and repressible

52
Q

Inducible

A

Roadblock. OFF until TURNED ON.

Tightly binds to the operator system and acts as a roadblock.

RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way.

To reverse: Inducer must bind to the repressor protein so that RNA polymerase can move down the gene.

53
Q

Repressible System

A

Always ON they get TURNED OFF

Repressive is inactive until it binds to a corepressor. This complex then binds to the operator site to prove my further transcription.

54
Q

Control of gene expression in eukaryotes

A

Transcription factors, gene amplification, enhancers

55
Q

Transcription factor

A

Transcription activating proteins that search the dna for specific dna binding motifs.

Dna binding domain binds to specific nucleotide sequence in the promoter region or to a dna response element (sequence of dna in the enhancer region that only binds to specific transcription factors)

56
Q

Enhancers

A

Response element grouped together are called enhancers. Controls one gene’s expression by multiple signals.

Can be up to 1000 base pairs away from the gene they regulate so they utilize the hairpin structure to make themselves closer in proximity.

57
Q

Histone acetylation

A

Transcription factors recruit other coactivators like histone acetylases that are involved in chromatin remodeling.

58
Q

Acetylation

A

Acetylation of histone proteins decrease the positive charge on lysine residues and weakens their interaction with dna resulting in a looser euchromatin confirmation easier for transcriptional machinery to access the DNA.

59
Q

Deacetylation

A

By histone deacetylases that remove acrylic groups from histones that tighten dna to heterochromatic

60
Q

DNA methylation

A

Involved with chromatin remodeling and regulation of gene expression.

Adds methyl groups to cytosine and adenine nucleotides soften linked with silencing of gene expression.

Heterochromatin heavily methylated.

Biochemistry (10 decks)

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